Header list of 1dt7.pdb file
Complete list - pr 27 Bytes
HEADER SIGNALING PROTEIN 11-JAN-00 1DT7
TITLE SOLUTION STRUCTURE OF THE C-TERMINAL NEGATIVE REGULATORY DOMAIN OF P53
TITLE 2 IN A COMPLEX WITH CA2+-BOUND S100B(BB)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: S100 CALCIUM-BINDING PROTEIN;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: BETA CHAIN;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: CELLULAR TUMOR ANTIGEN P53;
COMPND 8 CHAIN: X, Y;
COMPND 9 FRAGMENT: C-TERMINAL PEPTIDE;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE 3 ORGANISM_COMMON: NORWAY RAT;
SOURCE 4 ORGANISM_TAXID: 10116;
SOURCE 5 ORGAN: BRAIN;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: HMS174(DE3);
SOURCE 10 MOL_ID: 2;
SOURCE 11 SYNTHETIC: YES;
SOURCE 12 OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE
SOURCE 13 OF THIS PEPTIDE NATURALLY OCCURS IN HUMANS (HOMO SAPIENS).
KEYWDS S100B, P53, C-TERMINAL DOMAIN OF P53, CALCIUM-BINDING, EF-HAND, S100
KEYWDS 2 PROTEIN, FOUR HELIX BUNDLE, HELIX LOOP HELIX, SIGNALING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 40
AUTHOR R.R.RUSTANDI,D.M.BALDISSERI,D.J.WEBER
REVDAT 5 27-APR-16 1DT7 1 ATOM VERSN
REVDAT 4 24-FEB-09 1DT7 1 VERSN
REVDAT 3 04-SEP-07 1DT7 1 JRNL
REVDAT 2 01-APR-03 1DT7 1 JRNL
REVDAT 1 26-JUL-00 1DT7 0
JRNL AUTH R.R.RUSTANDI,D.M.BALDISSERI,D.J.WEBER
JRNL TITL STRUCTURE OF THE NEGATIVE REGULATORY DOMAIN OF P53 BOUND TO
JRNL TITL 2 S100B(BETABETA).
JRNL REF NAT.STRUCT.BIOL. V. 7 570 2000
JRNL REFN ISSN 1072-8368
JRNL PMID 10876243
JRNL DOI 10.1038/76797
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.851
REMARK 3 AUTHORS : BRUNGER, A.
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1DT7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-00.
REMARK 100 THE RCSB ID CODE IS RCSB010347.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 310
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : 25 MM
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 3-6 MM S100 (SUBUNIT
REMARK 210 CONCENTRATION), 0.1 MM EDTA, 0.34
REMARK 210 MM NAN3, 5 MM DTT, 17 MM NACL, 10
REMARK 210 MM D11-TRIS-HCL, 7% D2O, 6-13 MM
REMARK 210 CACL2, 4.8-10 MM P53 PEPTIDE
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 4D_13C-SEPARATED_NOESY; 4D_13C/
REMARK 210 15N-SEPARATED_NOESY; 3D_15N-
REMARK 210 SEPARATED_NOESY; 2D NOESY; 3D 13C
REMARK 210 -FILTER NOESY; 2D 13C-FILTER NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : DMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 2.0, NMRPIPE, X-PLOR
REMARK 210 3.851
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 40
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURE WITH THE LOWEST ENERGY
REMARK 210 AND THE LEAST RESTRAINT VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 22
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR
REMARK 210 SPECTROSCOPY
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, X, Y
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME;
REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 470 MODELS 1-40
REMARK 470 RES CSSEQI ATOMS
REMARK 470 GLU A 91 C O
REMARK 470 GLU B 91 C O
REMARK 470 GLU X 113 C O
REMARK 470 GLU Y 113 C O
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 HG SER B 41 HD1 HIS B 42 1.35
REMARK 500 O CYS B 84 H PHE B 88 1.43
REMARK 500 O CYS A 84 H PHE A 88 1.43
REMARK 500 O MET B 57 H ASP B 61 1.50
REMARK 500 O MET A 57 H ASP A 61 1.50
REMARK 500 OE1 GLU B 2 HZ2 LYS B 5 1.51
REMARK 500 OD2 ASP B 61 H GLY B 66 1.60
REMARK 500 OD2 ASP A 61 H GLY A 66 1.60
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 SER A 1 19.99 49.18
REMARK 500 1 GLU A 2 26.40 -76.22
REMARK 500 1 HIS A 90 72.34 -69.16
REMARK 500 1 SER B 1 19.98 49.48
REMARK 500 1 GLU B 2 25.59 -76.01
REMARK 500 1 HIS B 90 72.35 -69.26
REMARK 500 1 GLN X 100 116.40 57.19
REMARK 500 1 GLN Y 100 116.16 57.40
REMARK 500 2 GLU A 21 -73.25 -85.74
REMARK 500 2 LEU A 44 -144.54 -136.02
REMARK 500 2 GLU B 21 -73.50 -85.80
REMARK 500 2 LEU B 44 -144.27 -135.69
REMARK 500 2 LYS X 97 88.85 -170.51
REMARK 500 2 LYS Y 97 88.73 -170.56
REMARK 500 3 LEU A 3 -19.66 -46.17
REMARK 500 3 ASP A 23 68.73 -69.92
REMARK 500 3 LYS A 29 -27.21 -38.39
REMARK 500 3 LEU B 3 -19.75 -46.36
REMARK 500 3 ASP B 23 68.89 -69.92
REMARK 500 3 LYS B 29 -27.74 -38.20
REMARK 500 3 LEU X 94 -83.52 -90.03
REMARK 500 3 LYS X 95 -92.37 -153.37
REMARK 500 3 LEU Y 94 -83.16 -89.99
REMARK 500 3 LYS Y 95 -92.48 -153.81
REMARK 500 4 SER A 1 16.53 48.41
REMARK 500 4 LEU A 44 -145.06 -127.80
REMARK 500 4 SER B 1 16.32 48.40
REMARK 500 4 LEU B 44 -145.02 -127.75
REMARK 500 5 GLU A 21 -77.54 -89.99
REMARK 500 5 GLU A 45 106.04 -52.62
REMARK 500 5 GLU B 21 -78.04 -90.03
REMARK 500 5 GLU B 45 106.13 -52.54
REMARK 500 6 SER A 1 12.62 50.07
REMARK 500 6 SER B 1 12.37 50.03
REMARK 500 7 SER A 1 16.80 49.77
REMARK 500 7 LEU A 40 64.03 -103.60
REMARK 500 7 GLU A 89 99.66 -57.15
REMARK 500 7 SER B 1 16.93 49.90
REMARK 500 7 LEU B 40 63.56 -103.50
REMARK 500 7 GLU B 89 99.72 -57.34
REMARK 500 8 ASP A 23 46.97 -68.72
REMARK 500 8 LEU A 40 53.90 -113.33
REMARK 500 8 SER A 41 100.62 -57.94
REMARK 500 8 HIS A 42 -2.65 55.50
REMARK 500 8 LEU A 44 -144.63 -129.76
REMARK 500 8 ASP B 23 47.12 -68.62
REMARK 500 8 LEU B 40 53.92 -113.33
REMARK 500 8 SER B 41 100.70 -57.83
REMARK 500 8 HIS B 42 -2.62 55.43
REMARK 500 8 LEU B 44 -144.74 -129.79
REMARK 500
REMARK 500 THIS ENTRY HAS 248 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 1 CA A 114 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER A 18 O
REMARK 620 2 ASP A 23 O 91.1
REMARK 620 3 LYS A 26 O 145.0 55.1
REMARK 620 4 GLU A 31 OE1 135.9 113.8 73.9
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 1 CA A 115 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 61 OD1
REMARK 620 2 ASP A 63 N 85.4
REMARK 620 3 ASP A 63 OD2 154.5 79.8
REMARK 620 4 ASP A 65 OD1 62.3 122.5 109.2
REMARK 620 5 GLU A 67 O 90.2 174.2 102.9 51.8
REMARK 620 6 GLU A 72 OE1 113.1 76.8 83.7 157.7 108.5
REMARK 620 7 GLU A 72 OE2 154.0 99.4 50.3 130.8 86.2 45.1
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 1 CA B 116 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER B 18 O
REMARK 620 2 LYS B 26 O 144.4
REMARK 620 3 GLU B 31 OE1 138.3 74.8
REMARK 620 4 ASP B 23 O 91.1 55.3 116.7
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 1 CA B 117 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 61 OD1
REMARK 620 2 ASP B 63 N 84.9
REMARK 620 3 ASP B 63 OD2 153.7 79.5
REMARK 620 4 ASP B 65 OD1 62.1 121.6 109.1
REMARK 620 5 GLU B 67 O 90.6 173.8 103.1 52.3
REMARK 620 6 GLU B 72 OE1 113.0 76.6 83.9 158.6 109.1
REMARK 620 7 GLU B 72 OE2 154.5 99.1 50.4 131.7 86.8 45.2
REMARK 620 N 1 2 3 4 5 6
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 114
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 115
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 116
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 117
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4099 RELATED DB: BMRB
REMARK 900 CHEMICAL SHIFT ASSIGNMENT FOR S100B(BB)
REMARK 900 RELATED ID: 2169 RELATED DB: BMRB
REMARK 900 CHEMICAL SHIFT ASSIGNMENT FOR C-TERMINAL OF P53 PEPTIDE
DBREF 1DT7 A 0 91 UNP P04631 S100B_RAT 1 92
DBREF 1DT7 B 0 91 UNP P04631 S100B_RAT 1 92
DBREF 1DT7 X 92 113 UNP P04637 P53_HUMAN 367 388
DBREF 1DT7 Y 92 113 UNP P04637 P53_HUMAN 367 388
SEQRES 1 A 92 MET SER GLU LEU GLU LYS ALA MET VAL ALA LEU ILE ASP
SEQRES 2 A 92 VAL PHE HIS GLN TYR SER GLY ARG GLU GLY ASP LYS HIS
SEQRES 3 A 92 LYS LEU LYS LYS SER GLU LEU LYS GLU LEU ILE ASN ASN
SEQRES 4 A 92 GLU LEU SER HIS PHE LEU GLU GLU ILE LYS GLU GLN GLU
SEQRES 5 A 92 VAL VAL ASP LYS VAL MET GLU THR LEU ASP GLU ASP GLY
SEQRES 6 A 92 ASP GLY GLU CYS ASP PHE GLN GLU PHE MET ALA PHE VAL
SEQRES 7 A 92 SER MET VAL THR THR ALA CYS HIS GLU PHE PHE GLU HIS
SEQRES 8 A 92 GLU
SEQRES 1 B 92 MET SER GLU LEU GLU LYS ALA MET VAL ALA LEU ILE ASP
SEQRES 2 B 92 VAL PHE HIS GLN TYR SER GLY ARG GLU GLY ASP LYS HIS
SEQRES 3 B 92 LYS LEU LYS LYS SER GLU LEU LYS GLU LEU ILE ASN ASN
SEQRES 4 B 92 GLU LEU SER HIS PHE LEU GLU GLU ILE LYS GLU GLN GLU
SEQRES 5 B 92 VAL VAL ASP LYS VAL MET GLU THR LEU ASP GLU ASP GLY
SEQRES 6 B 92 ASP GLY GLU CYS ASP PHE GLN GLU PHE MET ALA PHE VAL
SEQRES 7 B 92 SER MET VAL THR THR ALA CYS HIS GLU PHE PHE GLU HIS
SEQRES 8 B 92 GLU
SEQRES 1 X 22 SER HIS LEU LYS SER LYS LYS GLY GLN SER THR SER ARG
SEQRES 2 X 22 HIS LYS LYS LEU MET PHE LYS THR GLU
SEQRES 1 Y 22 SER HIS LEU LYS SER LYS LYS GLY GLN SER THR SER ARG
SEQRES 2 Y 22 HIS LYS LYS LEU MET PHE LYS THR GLU
HET CA A 114 1
HET CA A 115 1
HET CA B 116 1
HET CA B 117 1
HETNAM CA CALCIUM ION
FORMUL 5 CA 4(CA 2+)
HELIX 1 1 GLU A 2 GLY A 19 1 18
HELIX 2 2 LYS A 29 LEU A 40 1 12
HELIX 3 3 GLU A 49 ASP A 61 1 13
HELIX 4 4 PHE A 70 PHE A 88 1 19
HELIX 5 5 GLU B 2 GLY B 19 1 18
HELIX 6 6 LYS B 29 LEU B 40 1 12
HELIX 7 7 GLU B 49 ASP B 61 1 13
HELIX 8 8 PHE B 70 PHE B 88 1 19
HELIX 9 9 GLN X 100 THR X 102 5 3
HELIX 10 10 SER X 103 GLU X 113 1 11
HELIX 11 11 GLN Y 100 THR Y 102 5 3
HELIX 12 12 SER Y 103 GLU Y 113 1 11
SHEET 1 A 2 LYS A 26 LYS A 28 0
SHEET 2 A 2 GLU A 67 ASP A 69 -1 O CYS A 68 N LEU A 27
SHEET 1 B 2 LYS B 26 LYS B 28 0
SHEET 2 B 2 GLU B 67 ASP B 69 -1 O CYS B 68 N LEU B 27
LINK O SER A 18 CA CA A 114 1555 1555 2.81
LINK O ASP A 23 CA CA A 114 1555 1555 2.00
LINK O LYS A 26 CA CA A 114 1555 1555 2.81
LINK OE1 GLU A 31 CA CA A 114 1555 1555 2.61
LINK OD1 ASP A 61 CA CA A 115 1555 1555 2.85
LINK N ASP A 63 CA CA A 115 1555 1555 2.67
LINK OD2 ASP A 63 CA CA A 115 1555 1555 2.88
LINK OD1 ASP A 65 CA CA A 115 1555 1555 2.86
LINK O GLU A 67 CA CA A 115 1555 1555 2.63
LINK OE1 GLU A 72 CA CA A 115 1555 1555 2.81
LINK OE2 GLU A 72 CA CA A 115 1555 1555 2.81
LINK O SER B 18 CA CA B 116 1555 1555 2.82
LINK O LYS B 26 CA CA B 116 1555 1555 2.81
LINK OE1 GLU B 31 CA CA B 116 1555 1555 2.56
LINK OD1 ASP B 61 CA CA B 117 1555 1555 2.86
LINK N ASP B 63 CA CA B 117 1555 1555 2.69
LINK OD2 ASP B 63 CA CA B 117 1555 1555 2.88
LINK OD1 ASP B 65 CA CA B 117 1555 1555 2.85
LINK O GLU B 67 CA CA B 117 1555 1555 2.62
LINK OE1 GLU B 72 CA CA B 117 1555 1555 2.81
LINK OE2 GLU B 72 CA CA B 117 1555 1555 2.80
LINK CA CA B 116 O ASP B 23 1555 1555 1.98
SITE 1 AC1 5 SER A 18 ASP A 23 LYS A 26 LEU A 27
SITE 2 AC1 5 GLU A 31
SITE 1 AC2 7 ASP A 61 GLU A 62 ASP A 63 GLY A 64
SITE 2 AC2 7 ASP A 65 GLU A 67 GLU A 72
SITE 1 AC3 4 SER B 18 ASP B 23 LYS B 26 GLU B 31
SITE 1 AC4 7 ASP B 61 GLU B 62 ASP B 63 GLY B 64
SITE 2 AC4 7 ASP B 65 GLU B 67 GLU B 72
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
Complete list - pr 27 Bytes