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