PDB Short entry for 2LP2 HEADER METAL BINDING PROTEIN 31-JAN-12 2LP2 TITLE SOLUTION STRUCTURE AND DYNAMICS OF HUMAN S100A1 PROTEIN MODIFIED AT TITLE 2 CYSTEINE 85 WITH HOMOCYSTEINE DISULFIDE BOND FORMATION IN CALCIUM TITLE 3 SATURATED FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN S100-A1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: S-100 PROTEIN ALPHA CHAIN, S-100 PROTEIN SUBUNIT ALPHA, S100 COMPND 5 CALCIUM-BINDING PROTEIN A1; COMPND 6 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: S100A1, S100A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET30A+ KEYWDS CALCIUM BOUND FORM, EF-HAND, CALCIUM BINDING, HELIX REORIENTATION, KEYWDS 2 SIGNALING PROTEIN, THIONYLATION, SMALL THIOLS, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.E.NOWAKOWSKI,L.JAREMKO,M.JAREMKO,K.ZDANOWSKI,A.EJCHART REVDAT 2 27-AUG-14 2LP2 1 JRNL REVDAT 1 20-FEB-13 2LP2 0 JRNL AUTH M.NOWAKOWSKI,K.RUSZCZYNSKA-BARTNIK,M.BUDZINSKA,L.JAREMKO, JRNL AUTH 2 M.JAREMKO,K.ZDANOWSKI,A.BIERZYNSKI,A.EJCHART JRNL TITL IMPACT OF CALCIUM BINDING AND THIONYLATION OF S100A1 PROTEIN JRNL TITL 2 ON ITS NUCLEAR MAGNETIC RESONANCE-DERIVED STRUCTURE AND JRNL TITL 3 BACKBONE DYNAMICS. JRNL REF BIOCHEMISTRY V. 52 1149 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 23351007 JRNL DOI 10.1021/BI3015407 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STANDARD SA.INP XPLOR NIH PROTOCOL REMARK 4 REMARK 4 2LP2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-FEB-12. REMARK 100 THE RCSB ID CODE IS RCSB102655. 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 : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-98% 13C; U-98% 15N] REMARK 210 S100A1 MONOMER, 10 MM CALCIUM REMARK 210 ION, 50 MM TRIS-D11, 0.1 MM REMARK 210 SODIUM AZIDE, 50 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 1 MM REMARK 210 [U-98% 15N] S100A1 MONOMER, 10 MM REMARK 210 CALCIUM ION, 50 MM TRIS-D11, 0.1 REMARK 210 MM SODIUM AZIDE, 50 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 1 MM REMARK 210 [U-98% 13C; U-98% 15N] S100A1 REMARK 210 MONOMER, 10 MM CALCIUM ION, 50 MM REMARK 210 TRIS-D11, 0.1 MM SODIUM AZIDE, 50 REMARK 210 MM SODIUM CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-15N HSQC REMARK 210 NH2 ONLY; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D CBCA(CO)NH; 3D C(CO) REMARK 210 NH; 3D HNCO; 3D HNCA; 3D HNCACB; REMARK 210 3D HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 3D 1H-15N NOESY; REMARK 210 2D 1H-15N HSQC (T1); 2D 1H-15N REMARK 210 HSQC (T2); 2D 15N-{1H} NOE REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 500 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITYPLUS; UNIFORM NMR REMARK 210 SYSTEM REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, NMRPIPE, SPARKY, X-PLOR_ REMARK 210 NIH, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 198 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 OD1 ASP B 66 H GLU B 68 1.59 REMARK 500 OD1 ASP A 66 H GLU A 68 1.59 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 LYS A 49 -32.48 67.59 REMARK 500 1 LYS B 49 -32.51 67.59 REMARK 500 3 LYS A 49 -35.80 71.09 REMARK 500 3 LYS B 49 -35.73 71.14 REMARK 500 4 GLU A 40 -60.01 -101.65 REMARK 500 6 SER A 42 -77.02 -110.80 REMARK 500 6 ASP A 62 72.01 -69.94 REMARK 500 6 SER B 42 -76.98 -110.89 REMARK 500 6 ASP B 62 72.05 -69.99 REMARK 500 9 SER A 2 24.65 34.82 REMARK 500 9 GLU A 40 -60.58 -102.15 REMARK 500 9 SER B 2 24.68 34.78 REMARK 500 9 GLU B 40 -60.63 -102.21 REMARK 500 12 SER A 42 -77.74 -108.49 REMARK 500 12 SER B 42 -77.72 -108.58 REMARK 500 13 SER A 2 18.88 38.41 REMARK 500 13 LYS A 49 -31.11 66.91 REMARK 500 13 SER B 2 18.79 38.51 REMARK 500 13 LYS B 49 -31.03 66.84 REMARK 500 15 LYS A 49 -28.72 65.27 REMARK 500 15 LYS B 49 -28.80 65.28 REMARK 500 17 GLU A 40 -60.01 -101.75 REMARK 500 17 GLU B 40 -60.02 -101.80 REMARK 500 19 LYS A 49 -40.21 72.19 REMARK 500 19 LYS B 49 -40.21 72.17 REMARK 500 20 SER A 42 -76.72 -111.57 REMARK 500 20 SER B 42 -76.77 -111.55 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 1 CA B 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 22 O REMARK 620 2 LYS B 27 O 162.1 REMARK 620 3 ASP B 24 O 95.9 77.2 REMARK 620 4 SER B 19 O 59.7 128.4 64.4 REMARK 620 5 GLU B 32 OE1 88.4 96.7 172.0 123.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 22 O REMARK 620 2 LYS A 27 O 162.1 REMARK 620 3 ASP A 24 O 95.9 77.1 REMARK 620 4 SER A 19 O 59.7 128.3 64.4 REMARK 620 5 GLU A 32 OE1 88.4 96.8 172.0 123.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 CA B 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 68 O REMARK 620 2 ASN B 64 OD1 145.4 REMARK 620 3 ASP B 62 OD1 78.1 102.1 REMARK 620 4 ASP B 66 OD1 67.4 78.5 80.3 REMARK 620 5 GLU B 73 OE2 92.4 122.2 86.4 157.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 CA A 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 68 O REMARK 620 2 ASN A 64 OD1 145.5 REMARK 620 3 ASP A 62 OD1 78.2 102.2 REMARK 620 4 ASP A 66 OD1 67.4 78.5 80.4 REMARK 620 5 GLU A 73 OE2 92.3 122.2 86.4 157.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HCS A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HCS B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2L0P RELATED DB: PDB REMARK 900 STRUCTURE OF THE SAME PROTEIN WITHOUT MODIFICATION AND IN REMARK 900 APO FORM REMARK 900 RELATED ID: 16360 RELATED DB: BMRB REMARK 900 NMR PARAMETERS OF THE SAME PROTEIN WITHOUT MODIFICATION AND REMARK 900 IN APO FORM REMARK 900 RELATED ID: 18230 RELATED DB: BMRB DBREF 2LP2 A 1 93 UNP P23297 S10A1_HUMAN 2 94 DBREF 2LP2 B 1 93 UNP P23297 S10A1_HUMAN 2 94 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 GLU LEU LEU GLN THR SEQRES 4 A 93 GLU LEU SER GLY PHE LEU ASP ALA GLN LYS ASP VAL ASP SEQRES 5 A 93 ALA VAL ASP LYS VAL MET LYS GLU LEU ASP GLU ASN GLY SEQRES 6 A 93 ASP GLY GLU VAL ASP PHE GLN GLU TYR 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 GLU LEU LEU GLN THR SEQRES 4 B 93 GLU LEU SER GLY PHE LEU ASP ALA GLN LYS ASP VAL ASP SEQRES 5 B 93 ALA VAL ASP LYS VAL MET LYS GLU LEU ASP GLU ASN GLY SEQRES 6 B 93 ASP GLY GLU VAL ASP PHE GLN GLU TYR 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 HCS A 201 16 HET CA A 202 1 HET CA A 203 1 HET HCS B 201 16 HET CA B 202 1 HET CA B 203 1 HETNAM HCS 2-AMINO-4-MERCAPTO-BUTYRIC ACID HETNAM CA CALCIUM ION FORMUL 3 HCS 2(C4 H9 N O2 S) FORMUL 4 CA 4(CA 2+) HELIX 1 1 SER A 2 GLU A 22 1 21 HELIX 2 2 SER A 29 LEU A 41 1 13 HELIX 3 3 SER A 42 LYS A 49 1 8 HELIX 4 4 ASP A 52 ASP A 62 1 11 HELIX 5 5 PHE A 71 GLU A 91 1 21 HELIX 6 6 SER B 2 GLU B 22 1 21 HELIX 7 7 SER B 29 LEU B 41 1 13 HELIX 8 8 SER B 42 LYS B 49 1 8 HELIX 9 9 ASP B 52 ASP B 62 1 11 HELIX 10 10 PHE B 71 GLU B 91 1 21 SHEET 1 A 2 LYS A 27 LEU A 28 0 SHEET 2 A 2 VAL A 69 ASP A 70 -1 O VAL A 69 N LEU A 28 SHEET 1 B 2 LYS B 27 LEU B 28 0 SHEET 2 B 2 VAL B 69 ASP B 70 -1 O VAL B 69 N LEU B 28 LINK O GLU B 22 CA CA B 202 1555 1555 2.32 LINK O GLU A 22 CA CA A 202 1555 1555 2.32 LINK O LYS B 27 CA CA B 202 1555 1555 2.41 LINK O LYS A 27 CA CA A 202 1555 1555 2.41 LINK O ASP B 24 CA CA B 202 1555 1555 2.47 LINK O ASP A 24 CA CA A 202 1555 1555 2.47 LINK O GLU B 68 CA CA B 203 1555 1555 2.49 LINK O GLU A 68 CA CA A 203 1555 1555 2.49 LINK O SER B 19 CA CA B 202 1555 1555 2.53 LINK O SER A 19 CA CA A 202 1555 1555 2.53 LINK OD1 ASN A 64 CA CA A 203 1555 1555 2.73 LINK OD1 ASN B 64 CA CA B 203 1555 1555 2.73 LINK OD1 ASP A 62 CA CA A 203 1555 1555 2.23 LINK OD1 ASP B 62 CA CA B 203 1555 1555 2.23 LINK OE1 GLU B 32 CA CA B 202 1555 1555 2.33 LINK OE1 GLU A 32 CA CA A 202 1555 1555 2.33 LINK OD1 ASP A 66 CA CA A 203 1555 1555 2.43 LINK OD1 ASP B 66 CA CA B 203 1555 1555 2.44 LINK OE2 GLU B 73 CA CA B 203 1555 1555 2.47 LINK OE2 GLU A 73 CA CA A 203 1555 1555 2.47 LINK SG CYS A 85 SD HCS A 201 1555 1555 2.02 LINK SG CYS B 85 SD HCS B 201 1555 1555 2.02 SITE 1 AC1 2 PHE A 44 CYS A 85 SITE 1 AC2 5 SER A 19 GLU A 22 ASP A 24 LYS A 27 SITE 2 AC2 5 GLU A 32 SITE 1 AC3 5 ASP A 62 ASN A 64 ASP A 66 GLU A 68 SITE 2 AC3 5 GLU A 73 SITE 1 AC4 2 PHE B 44 CYS B 85 SITE 1 AC5 5 SER B 19 GLU B 22 ASP B 24 LYS B 27 SITE 2 AC5 5 GLU B 32 SITE 1 AC6 5 ASP B 62 ASN B 64 ASP B 66 GLU B 68 SITE 2 AC6 5 GLU B 73 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