PDB Short entry for 1ZFS 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