Header list of 1yut.pdb file
Complete list - 2 20 Bytes
HEADER METAL BINDING PROTEIN 14-FEB-05 1YUT
TITLE SOLUTION STRUCTURE OF CALCIUM-S100A13 (MINIMIZED MEAN STRUCTURE)
CAVEAT 1YUT THERE ARE SOME CHIRALITY ERRORS IN CHAIN A AND B.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: S100 CALCIUM-BINDING PROTEIN A13;
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: S100A13;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21GOLD(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET21A;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21S100
KEYWDS S100A13, EF HAND CALCIUM-BINDING PROTEINS, COPPER(II), STRUCTURAL
KEYWDS 2 GENOMICS, STRUCTURAL PROTEOMICS IN EUROPE, SPINE, METAL BINDING
KEYWDS 3 PROTEIN
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR F.ARNESANO,L.BANCI,I.BERTINI,A.FANTONI,L.TENORI,M.S.VIEZZOLI,
AUTHOR 2 STRUCTURAL PROTEOMICS IN EUROPE (SPINE)
REVDAT 3 02-MAR-22 1YUT 1 REMARK LINK
REVDAT 2 24-FEB-09 1YUT 1 VERSN
REVDAT 1 18-OCT-05 1YUT 0
JRNL AUTH F.ARNESANO,L.BANCI,I.BERTINI,A.FANTONI,L.TENORI,M.S.VIEZZOLI
JRNL TITL STRUCTURAL INTERPLAY BETWEEN CALCIUM(II) AND COPPER(II)
JRNL TITL 2 BINDING TO S100A13 PROTEIN
JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 44 6341 2005
JRNL REFN ESSN 0570-0833
JRNL PMID 16145699
JRNL DOI 10.1002/ANIE.200500540
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DYANA 1.5, AMBER 6
REMARK 3 AUTHORS : GUNTERT ET AL. (DYANA), D.A. CASE ET AL. (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1YUT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-FEB-05.
REMARK 100 THE DEPOSITION ID IS D_1000031942.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 5.6
REMARK 210 IONIC STRENGTH : 20MM SODIUM ACETATE BUFFER
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.5MM 13C, 15N LABELED S100A13
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY; HNHA
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : RESTRAINED ENERGY MINIMIZATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 300
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 3D TECHNIQUES
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: 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 ALA A 3 55.60 71.58
REMARK 500 ARG A 29 103.25 62.03
REMARK 500 ASP A 31 -50.90 -159.27
REMARK 500 LEU A 50 77.95 -111.32
REMARK 500 ASP A 52 78.98 -175.91
REMARK 500 ASP A 92 73.33 -58.90
REMARK 500 LEU A 93 -51.73 -175.94
REMARK 500 ARG A 96 -46.50 -178.59
REMARK 500 LYS A 97 129.92 153.92
REMARK 500 ALA B 2 119.48 -171.92
REMARK 500 ALA B 3 100.19 28.07
REMARK 500 GLU B 27 -78.33 -88.46
REMARK 500 ARG B 29 101.53 51.98
REMARK 500 VAL B 35 49.48 -99.38
REMARK 500 ASN B 36 55.12 -156.05
REMARK 500 GLU B 37 -53.54 -141.74
REMARK 500 LYS B 51 60.33 -67.10
REMARK 500 ASP B 52 55.49 -177.77
REMARK 500 SER B 55 39.23 -89.88
REMARK 500 VAL B 65 -21.51 -35.71
REMARK 500 ASN B 74 49.42 98.95
REMARK 500 GLU B 75 -60.50 -90.14
REMARK 500 LYS B 89 79.09 -116.97
REMARK 500 LYS B 91 -2.57 -154.23
REMARK 500 ASP B 92 48.95 -92.94
REMARK 500 LYS B 94 -104.60 46.96
REMARK 500 ILE B 95 151.19 54.59
REMARK 500 LYS B 97 125.57 -175.32
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 MET A 1 ALA A 2 134.19
REMARK 500 LYS A 89 LYS A 90 -117.49
REMARK 500 ALA B 2 ALA B 3 143.10
REMARK 500 ALA B 3 GLU B 4 142.35
REMARK 500 GLY B 28 ARG B 29 137.15
REMARK 500 VAL B 35 ASN B 36 144.10
REMARK 500 LEU B 46 PRO B 47 -144.32
REMARK 500 ASP B 64 VAL B 65 -129.90
REMARK 500 ASN B 74 GLU B 75 112.62
REMARK 500 LYS B 91 ASP B 92 -145.53
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 PHE A 38 0.08 SIDE CHAIN
REMARK 500 ARG A 78 0.18 SIDE CHAIN
REMARK 500 ARG A 96 0.13 SIDE CHAIN
REMARK 500 PHE B 21 0.12 SIDE CHAIN
REMARK 500 TYR B 76 0.07 SIDE CHAIN
REMARK 500 ARG B 78 0.08 SIDE CHAIN
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 197 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 24 O
REMARK 620 2 GLU A 27 O 93.8
REMARK 620 3 GLY A 28 O 131.9 66.3
REMARK 620 4 ARG A 29 O 70.7 95.2 68.3
REMARK 620 5 SER A 32 O 88.8 172.8 107.1 79.4
REMARK 620 6 GLU A 37 OE1 114.1 106.1 113.5 157.4 78.7
REMARK 620 7 GLU A 37 OE2 73.1 74.5 133.4 141.5 112.7 54.7
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 198 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 64 OD1
REMARK 620 2 ASN A 66 OD1 78.2
REMARK 620 3 ASP A 68 OD1 82.9 90.1
REMARK 620 4 ASP A 68 OD2 128.9 75.7 54.3
REMARK 620 5 GLU A 70 O 103.4 159.8 70.3 88.4
REMARK 620 6 GLU A 75 OE1 121.8 127.6 136.3 109.0 69.2
REMARK 620 7 GLU A 75 OE2 89.2 80.5 168.9 127.8 119.5 54.8
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B 199 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA B 24 O
REMARK 620 2 GLY B 28 O 91.7
REMARK 620 3 ARG B 29 O 75.1 67.4
REMARK 620 4 SER B 32 O 99.2 134.2 72.7
REMARK 620 5 SER B 34 OG 159.3 95.5 125.5 89.6
REMARK 620 6 GLU B 37 OE1 79.6 138.0 144.9 87.8 82.1
REMARK 620 7 GLU B 37 OE2 75.7 82.4 136.8 143.4 86.1 55.6
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B 200 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 64 OD1
REMARK 620 2 ASP B 64 O 85.2
REMARK 620 3 ASP B 64 OD2 53.9 62.7
REMARK 620 4 ASN B 66 OD1 132.8 63.6 79.8
REMARK 620 5 ASP B 68 OD1 103.4 131.0 83.6 76.9
REMARK 620 6 GLU B 70 O 74.3 152.4 115.4 143.8 72.9
REMARK 620 7 GLU B 75 OE1 78.7 87.5 123.7 130.0 141.4 70.7
REMARK 620 8 GLU B 75 OE2 124.8 66.6 129.2 75.9 131.3 110.4 54.8
REMARK 620 N 1 2 3 4 5 6 7
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 197
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 198
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 199
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 200
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1YUR RELATED DB: PDB
REMARK 900 APO-S100A13, MINIMIZED AVERAGE STRUCTURE
REMARK 900 RELATED ID: 1YUS RELATED DB: PDB
REMARK 900 APO-S100A13, 25 ENSEMBLE STRUCTURES
REMARK 900 RELATED ID: 1YUU RELATED DB: PDB
REMARK 900 CALCIUM-S100A13, 25 ENSEMBLE STRUCTURES
REMARK 900 RELATED ID: CIRMMP11 RELATED DB: TARGETDB
DBREF 1YUT A 1 98 UNP Q99584 S10AD_HUMAN 1 98
DBREF 1YUT B 1 98 UNP Q99584 S10AD_HUMAN 1 98
SEQRES 1 A 98 MET ALA ALA GLU PRO LEU THR GLU LEU GLU GLU SER ILE
SEQRES 2 A 98 GLU THR VAL VAL THR THR PHE PHE THR PHE ALA ARG GLN
SEQRES 3 A 98 GLU GLY ARG LYS ASP SER LEU SER VAL ASN GLU PHE LYS
SEQRES 4 A 98 GLU LEU VAL THR GLN GLN LEU PRO HIS LEU LEU LYS ASP
SEQRES 5 A 98 VAL GLY SER LEU ASP GLU LYS MET LYS SER LEU ASP VAL
SEQRES 6 A 98 ASN GLN ASP SER GLU LEU LYS PHE ASN GLU TYR TRP ARG
SEQRES 7 A 98 LEU ILE GLY GLU LEU ALA LYS GLU ILE ARG LYS LYS LYS
SEQRES 8 A 98 ASP LEU LYS ILE ARG LYS LYS
SEQRES 1 B 98 MET ALA ALA GLU PRO LEU THR GLU LEU GLU GLU SER ILE
SEQRES 2 B 98 GLU THR VAL VAL THR THR PHE PHE THR PHE ALA ARG GLN
SEQRES 3 B 98 GLU GLY ARG LYS ASP SER LEU SER VAL ASN GLU PHE LYS
SEQRES 4 B 98 GLU LEU VAL THR GLN GLN LEU PRO HIS LEU LEU LYS ASP
SEQRES 5 B 98 VAL GLY SER LEU ASP GLU LYS MET LYS SER LEU ASP VAL
SEQRES 6 B 98 ASN GLN ASP SER GLU LEU LYS PHE ASN GLU TYR TRP ARG
SEQRES 7 B 98 LEU ILE GLY GLU LEU ALA LYS GLU ILE ARG LYS LYS LYS
SEQRES 8 B 98 ASP LEU LYS ILE ARG LYS LYS
HET CA A 197 1
HET CA A 198 1
HET CA B 199 1
HET CA B 200 1
HETNAM CA CALCIUM ION
FORMUL 3 CA 4(CA 2+)
HELIX 1 1 THR A 7 ARG A 25 1 19
HELIX 2 2 SER A 34 LEU A 46 1 13
HELIX 3 3 SER A 55 ASP A 64 1 10
HELIX 4 4 LYS A 72 LYS A 90 1 19
HELIX 5 5 THR B 7 ARG B 25 1 19
HELIX 6 6 GLU B 37 GLN B 45 1 9
HELIX 7 7 SER B 55 ASP B 64 1 10
HELIX 8 8 TRP B 77 ILE B 87 1 11
LINK O ALA A 24 CA CA A 197 1555 1555 2.32
LINK O GLU A 27 CA CA A 197 1555 1555 2.40
LINK O GLY A 28 CA CA A 197 1555 1555 2.38
LINK O ARG A 29 CA CA A 197 1555 1555 2.47
LINK O SER A 32 CA CA A 197 1555 1555 2.32
LINK OE1 GLU A 37 CA CA A 197 1555 1555 2.36
LINK OE2 GLU A 37 CA CA A 197 1555 1555 2.26
LINK OD1 ASP A 64 CA CA A 198 1555 1555 2.20
LINK OD1 ASN A 66 CA CA A 198 1555 1555 2.39
LINK OD1 ASP A 68 CA CA A 198 1555 1555 2.26
LINK OD2 ASP A 68 CA CA A 198 1555 1555 2.40
LINK O GLU A 70 CA CA A 198 1555 1555 2.34
LINK OE1 GLU A 75 CA CA A 198 1555 1555 2.32
LINK OE2 GLU A 75 CA CA A 198 1555 1555 2.31
LINK O ALA B 24 CA CA B 199 1555 1555 2.33
LINK O GLY B 28 CA CA B 199 1555 1555 2.31
LINK O ARG B 29 CA CA B 199 1555 1555 2.43
LINK O SER B 32 CA CA B 199 1555 1555 2.34
LINK OG SER B 34 CA CA B 199 1555 1555 2.43
LINK OE1 GLU B 37 CA CA B 199 1555 1555 2.28
LINK OE2 GLU B 37 CA CA B 199 1555 1555 2.29
LINK OD1 ASP B 64 CA CA B 200 1555 1555 2.29
LINK O ASP B 64 CA CA B 200 1555 1555 2.81
LINK OD2 ASP B 64 CA CA B 200 1555 1555 2.36
LINK OD1 ASN B 66 CA CA B 200 1555 1555 2.42
LINK OD1 ASP B 68 CA CA B 200 1555 1555 2.22
LINK O GLU B 70 CA CA B 200 1555 1555 2.42
LINK OE1 GLU B 75 CA CA B 200 1555 1555 2.29
LINK OE2 GLU B 75 CA CA B 200 1555 1555 2.33
CISPEP 1 ILE A 95 ARG A 96 0 -9.33
CISPEP 2 ARG A 96 LYS A 97 0 5.10
CISPEP 3 LYS A 97 LYS A 98 0 11.18
SITE 1 AC1 6 ALA A 24 GLU A 27 GLY A 28 ARG A 29
SITE 2 AC1 6 SER A 32 GLU A 37
SITE 1 AC2 5 ASP A 64 ASN A 66 ASP A 68 GLU A 70
SITE 2 AC2 5 GLU A 75
SITE 1 AC3 6 ALA B 24 GLY B 28 ARG B 29 SER B 32
SITE 2 AC3 6 SER B 34 GLU B 37
SITE 1 AC4 5 ASP B 64 ASN B 66 ASP B 68 GLU B 70
SITE 2 AC4 5 GLU B 75
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
Complete list - 2 20 Bytes