Header list of 1zfs.pdb file
Complete list - r 2 2 Bytes
HEADER METAL BINDING PROTEIN 20-APR-05 1ZFS
TITLE SOLUTION STRUCTURE OF S100A1 BOUND TO CALCIUM
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: S-100 PROTEIN, ALPHA CHAIN;
COMPND 3 CHAIN: A, B;
COMPND 4 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 GENE: S100A1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HMS 174;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11B
KEYWDS S100, NONCOVALENT HOMODIMER, X-TYPE 4 HELIX BUNDLE, CALCIUM BINDING,
KEYWDS 2 CONFORMATIONAL CHANGE, METAL BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 19
AUTHOR N.T.WRIGHT,K.M.VARNEY,D.J.WEBER
REVDAT 3 02-MAR-22 1ZFS 1 REMARK LINK
REVDAT 2 24-FEB-09 1ZFS 1 VERSN
REVDAT 1 11-APR-06 1ZFS 0
JRNL AUTH N.T.WRIGHT,K.M.VARNEY,K.C.ELLIS,J.MARKOWITZ,R.K.GITTI,
JRNL AUTH 2 D.B.ZIMMER,D.J.WEBER
JRNL TITL THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF CA(2+)-BOUND
JRNL TITL 2 S100A1 AS DETERMINED BY NMR SPECTROSCOPY
JRNL REF J.MOL.BIOL. V. 353 410 2006
JRNL REFN ISSN 0022-2836
JRNL PMID 16169012
JRNL DOI 10.1016/J.JMB.2005.08.027
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 2.9.3, X-PLOR 2.9.3
REMARK 3 AUTHORS : C.D. SCHWIETERS, J.J. KUSZEWSKI, N. TJANDRA, G.M.
REMARK 3 CLORE (X-PLOR), C.D. SCHWIETERS, J.J. KUSZEWSKI,
REMARK 3 N. TJANDRA, G.M. CLORE (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1ZFS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-05.
REMARK 100 THE DEPOSITION ID IS D_1000032667.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 310
REMARK 210 PH : 7.2
REMARK 210 IONIC STRENGTH : 15 MM
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.5-3 MM S100A1 MONOMER, U-15N,
REMARK 210 13C, 0.35 MM NAN3, 15 MM NACL,
REMARK 210 20 MM CACL2, 25 MM TRIS, 25 MM
REMARK 210 DTT, 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 4D_13C-SEPARATED_NOESY;
REMARK 210 4D_13C/15N-SEPARATED_NOESY; 3D_
REMARK 210 15N-SEPARATED_NOESY; HNHA
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : DMX; AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED
REMARK 210 ANNEALING (DGSA)
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 19
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK:
REMARK 210 RDC DATA USING RADIALLY AND AXIALLY COMPRESSED ACRYLAMIDE GELS
REMARK 210 WERE ADDED INTO STRUCTURE CALCULATIONS.
REMARK 210 H-BONDS WERE DETERMINED USING HYDROGEN EXCHANGE EXPERIMENTS
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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 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 O ASP A 62 H GLY A 65 1.44
REMARK 500 O ASP B 62 H GLY B 65 1.44
REMARK 500 O MET B 58 H ASP B 62 1.47
REMARK 500 O MET A 58 H ASP A 62 1.47
REMARK 500 HG1 THR A 10 O GLU B 3 1.49
REMARK 500 O SER B 2 H THR B 6 1.50
REMARK 500 O ASP B 70 H GLN B 72 1.51
REMARK 500 O SER A 2 H THR A 6 1.51
REMARK 500 O ASP A 70 H GLN A 72 1.51
REMARK 500 H LEU A 4 OE1 GLU B 40 1.52
REMARK 500 OE1 GLU A 40 H LEU B 4 1.55
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 VAL A 47 -52.90 -163.53
REMARK 500 1 ASP A 62 42.42 -81.95
REMARK 500 1 PHE A 71 -42.25 62.60
REMARK 500 1 VAL B 47 -52.92 -163.53
REMARK 500 1 ASP B 62 42.64 -81.88
REMARK 500 1 PHE B 71 -42.55 62.74
REMARK 500 2 SER A 2 -66.70 -103.49
REMARK 500 2 VAL A 47 -53.76 -160.24
REMARK 500 2 LEU A 61 -160.47 -68.53
REMARK 500 2 ASP A 62 58.14 -64.38
REMARK 500 2 GLU A 63 37.35 -74.24
REMARK 500 2 PHE A 71 -57.30 61.01
REMARK 500 2 SER B 2 -66.43 -103.47
REMARK 500 2 VAL B 47 -53.88 -160.37
REMARK 500 2 LEU B 61 -160.43 -68.50
REMARK 500 2 ASP B 62 57.97 -64.46
REMARK 500 2 GLU B 63 37.61 -74.30
REMARK 500 2 ASP B 70 30.27 -84.15
REMARK 500 2 PHE B 71 -57.24 60.90
REMARK 500 3 PHE A 44 -70.01 -79.97
REMARK 500 3 ASP A 46 92.46 -58.03
REMARK 500 3 ASP A 62 44.62 -69.17
REMARK 500 3 PHE A 71 -60.63 82.01
REMARK 500 3 ASP B 46 92.73 -58.02
REMARK 500 3 LEU B 61 -70.10 -80.46
REMARK 500 3 ASP B 62 44.46 -68.74
REMARK 500 3 PHE B 71 -60.49 82.16
REMARK 500 4 TYR A 26 48.58 -94.37
REMARK 500 4 VAL A 47 -69.38 -162.37
REMARK 500 4 PHE A 71 -63.94 81.80
REMARK 500 4 TYR B 26 47.92 -94.00
REMARK 500 4 VAL B 47 -68.87 -162.35
REMARK 500 4 PHE B 71 -64.05 81.99
REMARK 500 5 LYS A 25 -13.21 -42.88
REMARK 500 5 ASP A 46 80.90 -62.95
REMARK 500 5 LEU A 61 -70.04 -81.71
REMARK 500 5 ASP A 62 34.87 -74.49
REMARK 500 5 PHE A 71 -40.94 62.31
REMARK 500 5 LYS B 25 -13.50 -43.10
REMARK 500 5 ASP B 46 80.44 -62.65
REMARK 500 5 LEU B 61 -70.12 -81.65
REMARK 500 5 ASP B 62 35.96 -74.62
REMARK 500 5 PHE B 71 -40.88 62.30
REMARK 500 6 ASP A 24 38.28 -91.02
REMARK 500 6 VAL A 47 -52.66 -161.70
REMARK 500 6 ASP A 50 79.29 -101.46
REMARK 500 6 ASP A 62 39.29 -67.68
REMARK 500 6 GLU A 63 -8.58 -58.14
REMARK 500 6 PHE A 71 -60.81 146.06
REMARK 500 6 ASP B 24 38.34 -90.72
REMARK 500
REMARK 500 THIS ENTRY HAS 181 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 CA A 104 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER A 19 OG
REMARK 620 2 SER A 19 O 89.0
REMARK 620 3 ASP A 24 O 129.8 87.1
REMARK 620 4 LYS A 27 O 120.2 145.9 61.2
REMARK 620 5 GLU A 32 OE2 116.9 62.4 105.2 111.6
REMARK 620 6 GLU A 32 OE1 114.9 108.0 113.9 77.1 46.0
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 103 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LEU A 61 O
REMARK 620 2 ASP A 62 OD1 78.4
REMARK 620 3 ASP A 66 OD2 130.6 80.7
REMARK 620 4 GLU A 68 O 126.2 48.0 47.8
REMARK 620 5 GLU A 73 OE1 44.6 102.9 171.9 139.6
REMARK 620 6 GLU A 73 OE2 75.3 147.3 131.7 154.7 44.4
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B 102 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER B 19 OG
REMARK 620 2 SER B 19 O 85.0
REMARK 620 3 ASP B 24 O 131.3 81.8
REMARK 620 4 LYS B 27 O 129.9 141.0 62.6
REMARK 620 5 GLU B 32 OE1 116.9 102.6 111.7 78.5
REMARK 620 6 GLU B 32 OE2 112.9 57.8 98.8 110.2 45.0
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B 101 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LEU B 61 O
REMARK 620 2 ASP B 62 OD1 78.4
REMARK 620 3 ASP B 66 OD2 131.1 80.8
REMARK 620 4 GLU B 68 O 126.2 48.1 47.8
REMARK 620 5 GLU B 73 OE2 75.3 146.9 132.0 154.3
REMARK 620 6 GLU B 73 OE1 44.6 102.6 172.5 139.0 44.3
REMARK 620 N 1 2 3 4 5
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 102
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 103
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 104
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6583 RELATED DB: BMRB
REMARK 900 CHEMICAL SHIFT ASSIGNMENTS OF CA2+-S100A1
REMARK 900 RELATED ID: 1K2H RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE SAME PROTEIN, APO FORM
DBREF 1ZFS A 1 93 UNP P35467 S10A1_RAT 1 93
DBREF 1ZFS B 1 93 UNP P35467 S10A1_RAT 1 93
SEQRES 1 A 93 GLY SER GLU LEU GLU THR ALA MET GLU THR LEU ILE ASN
SEQRES 2 A 93 VAL PHE HIS ALA HIS SER GLY LYS GLU GLY ASP LYS TYR
SEQRES 3 A 93 LYS LEU SER LYS LYS GLU LEU LYS ASP LEU LEU GLN THR
SEQRES 4 A 93 GLU LEU SER SER PHE LEU ASP VAL GLN LYS ASP ALA ASP
SEQRES 5 A 93 ALA VAL ASP LYS ILE MET LYS GLU LEU ASP GLU ASN GLY
SEQRES 6 A 93 ASP GLY GLU VAL ASP PHE GLN GLU PHE VAL VAL LEU VAL
SEQRES 7 A 93 ALA ALA LEU THR VAL ALA CYS ASN ASN PHE PHE TRP GLU
SEQRES 8 A 93 ASN SER
SEQRES 1 B 93 GLY SER GLU LEU GLU THR ALA MET GLU THR LEU ILE ASN
SEQRES 2 B 93 VAL PHE HIS ALA HIS SER GLY LYS GLU GLY ASP LYS TYR
SEQRES 3 B 93 LYS LEU SER LYS LYS GLU LEU LYS ASP LEU LEU GLN THR
SEQRES 4 B 93 GLU LEU SER SER PHE LEU ASP VAL GLN LYS ASP ALA ASP
SEQRES 5 B 93 ALA VAL ASP LYS ILE MET LYS GLU LEU ASP GLU ASN GLY
SEQRES 6 B 93 ASP GLY GLU VAL ASP PHE GLN GLU PHE VAL VAL LEU VAL
SEQRES 7 B 93 ALA ALA LEU THR VAL ALA CYS ASN ASN PHE PHE TRP GLU
SEQRES 8 B 93 ASN SER
HET CA A 103 1
HET CA A 104 1
HET CA B 101 1
HET CA B 102 1
HETNAM CA CALCIUM ION
FORMUL 3 CA 4(CA 2+)
HELIX 1 1 SER A 2 SER A 19 1 18
HELIX 2 2 GLY A 20 GLU A 22 5 3
HELIX 3 3 LYS A 30 LEU A 41 1 12
HELIX 4 4 ASP A 50 ASP A 62 1 13
HELIX 5 5 PHE A 71 ASN A 92 1 22
HELIX 6 6 SER B 2 SER B 19 1 18
HELIX 7 7 GLY B 20 GLU B 22 5 3
HELIX 8 8 LYS B 30 LEU B 41 1 12
HELIX 9 9 ASP B 50 ASP B 62 1 13
HELIX 10 10 PHE B 71 ASN B 92 1 22
SHEET 1 A 2 LYS A 27 SER A 29 0
SHEET 2 A 2 GLU A 68 ASP A 70 -1 O VAL A 69 N LEU A 28
SHEET 1 B 2 LYS B 27 SER B 29 0
SHEET 2 B 2 GLU B 68 ASP B 70 -1 O VAL B 69 N LEU B 28
LINK OG SER A 19 CA CA A 104 1555 1555 1.93
LINK O SER A 19 CA CA A 104 1555 1555 2.55
LINK O ASP A 24 CA CA A 104 1555 1555 2.31
LINK O LYS A 27 CA CA A 104 1555 1555 2.81
LINK OE2 GLU A 32 CA CA A 104 1555 1555 2.44
LINK OE1 GLU A 32 CA CA A 104 1555 1555 2.94
LINK O LEU A 61 CA CA A 103 1555 1555 3.33
LINK OD1 ASP A 62 CA CA A 103 1555 1555 2.87
LINK OD2 ASP A 66 CA CA A 103 1555 1555 2.98
LINK O GLU A 68 CA CA A 103 1555 1555 2.86
LINK OE1 GLU A 73 CA CA A 103 1555 1555 2.78
LINK OE2 GLU A 73 CA CA A 103 1555 1555 2.91
LINK OG SER B 19 CA CA B 102 1555 1555 1.85
LINK O SER B 19 CA CA B 102 1555 1555 2.74
LINK O ASP B 24 CA CA B 102 1555 1555 2.36
LINK O LYS B 27 CA CA B 102 1555 1555 2.70
LINK OE1 GLU B 32 CA CA B 102 1555 1555 2.96
LINK OE2 GLU B 32 CA CA B 102 1555 1555 2.60
LINK O LEU B 61 CA CA B 101 1555 1555 3.33
LINK OD1 ASP B 62 CA CA B 101 1555 1555 2.86
LINK OD2 ASP B 66 CA CA B 101 1555 1555 2.97
LINK O GLU B 68 CA CA B 101 1555 1555 2.85
LINK OE2 GLU B 73 CA CA B 101 1555 1555 2.91
LINK OE1 GLU B 73 CA CA B 101 1555 1555 2.79
SITE 1 AC1 6 LEU B 61 ASP B 62 ASP B 66 GLU B 68
SITE 2 AC1 6 VAL B 69 GLU B 73
SITE 1 AC2 5 SER B 19 ASP B 24 LYS B 27 LEU B 28
SITE 2 AC2 5 GLU B 32
SITE 1 AC3 6 LEU A 61 ASP A 62 ASP A 66 GLU A 68
SITE 2 AC3 6 VAL A 69 GLU A 73
SITE 1 AC4 4 SER A 19 ASP A 24 LYS A 27 GLU A 32
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 - r 2 2 Bytes