10 20 30 40 50 60 70 80 1YUT - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER METAL BINDING PROTEIN 14-FEB-05 1YUT
TITLE SOLUTION STRUCTURE OF CALCIUM-S100A13 (MINIMIZED MEAN TITLE 2 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), NMR KEYWDS 2 STRUCTURE, STRUCTURAL GENOMICS, STRUCTURAL PROTEOMICS IN KEYWDS 3 EUROPE, SPINE, METAL BINDING PROTEIN
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR F.ARNESANO,L.BANCI,I.BERTINI,A.FANTONI,L.TENORI, AUTHOR 2 M.S.VIEZZOLI,STRUCTURAL PROTEOMICS IN EUROPE (SPINE)
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, JRNL AUTH 2 M.S.VIEZZOLI JRNL TITL STRUCTURAL INTERPLAY BETWEEN CALCIUM(II) AND JRNL TITL 2 COPPER(II) BINDING TO S100A13 PROTEIN JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 44 6341 2005 JRNL REFN ISSN 1433-7851 JRNL PMID 16145699 JRNL DOI 10.1002/ANIE.200500540
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 6 REMARK 3 AUTHORS : D.A. CASE ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1YUT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-FEB-05. REMARK 100 THE RCSB ID CODE IS RCSB031942.
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_ REMARK 210 13C-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 : DYANA 1.5 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 REMARK 210 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LYS A 97 134.3 ALPHA-CARBON REMARK 500 LYS A 98 124.8 ALPHA-CARBON REMARK 500 LYS B 94 121.2 ALPHA-CARBON 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 ARG A 29 O 70.7 95.2 REMARK 620 4 SER A 32 O 88.8 172.8 79.4 REMARK 620 5 GLU A 37 OE1 114.1 106.1 157.4 78.7 REMARK 620 6 GLU A 37 OE2 73.1 74.5 141.5 112.7 54.7 REMARK 620 7 GLY A 28 O 131.9 66.3 68.3 107.1 113.5 133.4 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 GLU A 70 O 103.4 159.8 70.3 REMARK 620 5 GLU A 75 OE1 121.8 127.6 136.3 69.2 REMARK 620 6 GLU A 75 OE2 89.2 80.5 168.9 119.5 54.8 REMARK 620 7 ASP A 68 OD2 128.9 75.7 54.3 88.4 109.0 127.8 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 ARG B 29 O 75.1 REMARK 620 3 SER B 32 O 99.2 72.7 REMARK 620 4 GLU B 37 OE1 79.6 144.9 87.8 REMARK 620 5 GLU B 37 OE2 75.7 136.8 143.4 55.6 REMARK 620 6 GLY B 28 O 91.7 67.4 134.2 138.0 82.4 REMARK 620 7 SER B 34 OG 159.3 125.5 89.6 82.1 86.1 95.5 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 ASN B 66 OD1 132.8 REMARK 620 3 ASP B 68 OD1 103.4 76.9 REMARK 620 4 GLU B 70 O 74.3 143.8 72.9 REMARK 620 5 GLU B 75 OE1 78.7 130.0 141.4 70.7 REMARK 620 6 GLU B 75 OE2 124.8 75.9 131.3 110.4 54.8 REMARK 620 7 ASP B 64 O 85.2 63.6 131.0 152.4 87.5 66.6 REMARK 620 8 ASP B 64 OD2 53.9 79.8 83.6 115.4 123.7 129.2 62.7 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 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 198 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 199 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 CA CA A 197 O ALA A 24 1555 1555 2.32 LINK CA CA A 197 O GLU A 27 1555 1555 2.40 LINK CA CA A 197 O ARG A 29 1555 1555 2.47 LINK CA CA A 197 O SER A 32 1555 1555 2.32 LINK CA CA A 197 OE1 GLU A 37 1555 1555 2.36 LINK CA CA A 197 OE2 GLU A 37 1555 1555 2.26 LINK CA CA A 198 OD1 ASP A 64 1555 1555 2.20 LINK CA CA A 198 OD1 ASN A 66 1555 1555 2.39 LINK CA CA A 198 OD1 ASP A 68 1555 1555 2.26 LINK CA CA A 198 O GLU A 70 1555 1555 2.34 LINK CA CA A 198 OE1 GLU A 75 1555 1555 2.32 LINK CA CA A 198 OE2 GLU A 75 1555 1555 2.31 LINK CA CA B 199 O ALA B 24 1555 1555 2.33 LINK CA CA B 199 O ARG B 29 1555 1555 2.43 LINK CA CA B 199 O SER B 32 1555 1555 2.34 LINK CA CA B 199 OE1 GLU B 37 1555 1555 2.28 LINK CA CA B 199 OE2 GLU B 37 1555 1555 2.29 LINK CA CA B 200 OD1 ASP B 64 1555 1555 2.29 LINK CA CA B 200 OD1 ASN B 66 1555 1555 2.42 LINK CA CA B 200 OD1 ASP B 68 1555 1555 2.22 LINK CA CA B 200 O GLU B 70 1555 1555 2.42 LINK CA CA B 200 OE1 GLU B 75 1555 1555 2.29 LINK CA CA B 200 OE2 GLU B 75 1555 1555 2.33 LINK CA CA A 197 O GLY A 28 1555 1555 2.38 LINK CA CA A 198 OD2 ASP A 68 1555 1555 2.40 LINK CA CA B 199 O GLY B 28 1555 1555 2.31 LINK CA CA B 199 OG SER B 34 1555 1555 2.43 LINK CA CA B 200 O ASP B 64 1555 1555 2.81 LINK CA CA B 200 OD2 ASP B 64 1555 1555 2.36
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