PDB Short entry for 2WC8 HEADER METAL BINDING PROTEIN 10-MAR-09 2WC8 TITLE S100A12 COMPLEX WITH ZINC IN THE ABSENCE OF CALCIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN S100-A12; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: RESIDUES 2-92; COMPND 5 SYNONYM: S100 CALCIUM-BINDING PROTEIN A12, CALGRANULIN-C, CGRP, COMPND 6 NEUTROPHIL S100 PROTEIN, CALCIUM-BINDING PROTEIN IN AMNIOTIC FLUID1, COMPND 7 P6, CAGC, CAAF1S100A12; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PQE60 KEYWDS CALCIUM SIGNALLING, EF-HAND, CALCIUM FREE, S100 PROTEIN, HOST- KEYWDS 2 PARASITE RESPONSE, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR O.V.MOROZ,E.V.BLAGOVA,A.J.WILKINSON,K.S.WILSON,I.B.BRONSTEIN REVDAT 5 13-DEC-23 2WC8 1 REMARK LINK REVDAT 4 25-MAR-20 2WC8 1 REMARK REVDAT 3 13-JUL-11 2WC8 1 VERSN REVDAT 2 11-AUG-09 2WC8 1 JRNL REVDAT 1 23-JUN-09 2WC8 0 JRNL AUTH O.V.MOROZ,E.V.BLAGOVA,A.J.WILKINSON,K.S.WILSON,I.B.BRONSTEIN JRNL TITL THE CRYSTAL STRUCTURES OF HUMAN S100A12 IN APO FORM AND IN JRNL TITL 2 COMPLEX WITH ZINC: NEW INSIGHTS INTO S100A12 JRNL TITL 3 OLIGOMERISATION. JRNL REF J.MOL.BIOL. V. 391 536 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19501594 JRNL DOI 10.1016/J.JMB.2009.06.004 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.V.MOROZ,A.A.ANTSON,G.N.MURSHUDOV,N.J.MAITLAND,G.G.DODSON, REMARK 1 AUTH 2 K.S.WILSON,I.SKIBSHOJ,E.M.LUKANIDIN,I.B.BRONSTEIN REMARK 1 TITL THE THREE-DIMENSIONAL STRUCTURE OF HUMAN S100A12. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 57 20 2001 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 11134923 REMARK 1 DOI 10.1107/S090744490001458X REMARK 1 REFERENCE 2 REMARK 1 AUTH O.V.MOROZ,A.A.ANTSON,S.J.GRIST,N.J.MAITLAND,G.G.DODSON, REMARK 1 AUTH 2 K.S.WILSON,E.LUKANIDIN,I.B.BRONSTEIN REMARK 1 TITL STRUCTURE OF THE HUMAN S100A12-COPPER COMPLEX: IMPLICATIONS REMARK 1 TITL 2 FOR HOST-PARASITE DEFENCE. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 59 859 2003 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 12777802 REMARK 1 DOI 10.1107/S0907444903004700 REMARK 1 REFERENCE 3 REMARK 1 AUTH O.V.MOROZ,A.A.ANTSON,E.J.DODSON,H.J.BURRELL,S.J.GRIST, REMARK 1 AUTH 2 R.M.LLOYD,N.J.MAITLAND,G.G.DODSON,K.S.WILSON,E.LUKANIDIN, REMARK 1 AUTH 3 I.B.BRONSTEIN REMARK 1 TITL THE STRUCTURE OF S100A12 IN A HEXAMERIC FORM AND ITS REMARK 1 TITL 2 PROPOSED ROLE IN RECEPTOR SIGNALLING. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 407 2002 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 11856825 REMARK 1 DOI 10.1107/S0907444901021278 REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0082 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 29192 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1546 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.88 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2092 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2928 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 509 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.09000 REMARK 3 B22 (A**2) : 0.94000 REMARK 3 B33 (A**2) : 0.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.580 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3039 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2006 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4092 ; 1.577 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4954 ; 1.014 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 367 ; 5.150 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 154 ;38.863 ;26.104 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 575 ;15.871 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;28.922 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 465 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3364 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 576 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1834 ; 0.876 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 751 ; 0.273 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2951 ; 1.512 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1205 ; 2.513 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1141 ; 3.860 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 91 REMARK 3 ORIGIN FOR THE GROUP (A): -14.6887 -26.0633 10.9334 REMARK 3 T TENSOR REMARK 3 T11: 0.0432 T22: 0.0449 REMARK 3 T33: 0.0548 T12: 0.0066 REMARK 3 T13: -0.0006 T23: -0.0203 REMARK 3 L TENSOR REMARK 3 L11: 1.4145 L22: 1.7042 REMARK 3 L33: 2.4286 L12: 0.8443 REMARK 3 L13: -0.8198 L23: -0.3296 REMARK 3 S TENSOR REMARK 3 S11: -0.1245 S12: 0.1255 S13: -0.1335 REMARK 3 S21: -0.1791 S22: 0.0107 S23: -0.0416 REMARK 3 S31: 0.2489 S32: -0.0250 S33: 0.1137 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 0 B 91 REMARK 3 ORIGIN FOR THE GROUP (A): -2.6443 -13.0957 15.5945 REMARK 3 T TENSOR REMARK 3 T11: 0.0178 T22: 0.0341 REMARK 3 T33: 0.0358 T12: 0.0005 REMARK 3 T13: -0.0211 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 1.5793 L22: 1.5295 REMARK 3 L33: 2.9024 L12: 0.5867 REMARK 3 L13: -0.7838 L23: -0.8098 REMARK 3 S TENSOR REMARK 3 S11: 0.0434 S12: -0.1622 S13: -0.0077 REMARK 3 S21: 0.1111 S22: -0.0783 S23: -0.1891 REMARK 3 S31: -0.0817 S32: 0.2425 S33: 0.0349 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 0 C 91 REMARK 3 ORIGIN FOR THE GROUP (A): -18.3459 2.4451 -1.5699 REMARK 3 T TENSOR REMARK 3 T11: 0.0610 T22: 0.0397 REMARK 3 T33: 0.0492 T12: -0.0061 REMARK 3 T13: -0.0230 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 2.2746 L22: 2.1546 REMARK 3 L33: 1.0720 L12: -1.2251 REMARK 3 L13: -0.3542 L23: 0.5040 REMARK 3 S TENSOR REMARK 3 S11: 0.0808 S12: 0.2474 S13: -0.1748 REMARK 3 S21: -0.2166 S22: -0.0930 S23: 0.2596 REMARK 3 S31: 0.0116 S32: -0.1022 S33: 0.0122 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D -1 D 91 REMARK 3 ORIGIN FOR THE GROUP (A): -14.3004 17.0578 9.7502 REMARK 3 T TENSOR REMARK 3 T11: 0.0383 T22: 0.0356 REMARK 3 T33: 0.0336 T12: -0.0119 REMARK 3 T13: 0.0028 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 2.5993 L22: 2.0389 REMARK 3 L33: 1.3250 L12: -0.6262 REMARK 3 L13: -0.3267 L23: 0.8733 REMARK 3 S TENSOR REMARK 3 S11: -0.0107 S12: -0.0742 S13: 0.2363 REMARK 3 S21: -0.0083 S22: 0.0877 S23: -0.1768 REMARK 3 S31: -0.1105 S32: 0.1787 S33: -0.0770 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES RESIDUAL ONLY REMARK 4 REMARK 4 2WC8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1290039008. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30804 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.90000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1E8A REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M TRI-AMMONIIUM CITRATE PH 7.0, 34% REMARK 280 PEG 3350 MME, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 26.49550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.86250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.91500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.86250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.49550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.91500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -124.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -128.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -3 REMARK 465 GLY A -2 REMARK 465 GLY A -1 REMARK 465 ASN A 63 REMARK 465 GLN A 64 REMARK 465 ASP A 65 REMARK 465 GLU A 66 REMARK 465 MET B -3 REMARK 465 GLY B -2 REMARK 465 GLY B -1 REMARK 465 MET C -3 REMARK 465 GLY C -2 REMARK 465 GLY C -1 REMARK 465 ASP C 61 REMARK 465 MET D -3 REMARK 465 GLY D -2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS B 90 CG CD CE NZ REMARK 470 LYS C 48 CD CE NZ REMARK 470 GLU C 66 CD OE1 OE2 REMARK 470 LYS D 48 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 N ALA C 62 O HOH C 2088 2.06 REMARK 500 O HOH A 2037 O HOH A 2089 2.10 REMARK 500 O HOH B 2049 O HOH B 2123 2.13 REMARK 500 O HOH B 2052 O HOH B 2128 2.14 REMARK 500 O HOH C 2039 O HOH C 2044 2.14 REMARK 500 O HOH A 2116 O HOH A 2120 2.15 REMARK 500 O HOH B 2022 O HOH B 2066 2.16 REMARK 500 O HOH A 2010 O HOH C 2021 2.17 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 ZN A 95 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 15 NE2 REMARK 620 2 ASP A 25 OD1 99.5 REMARK 620 3 HIS B 85 NE2 106.6 114.4 REMARK 620 4 HIS B 89 NE2 111.1 115.4 109.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 92 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 18 O REMARK 620 2 LYS A 21 O 102.9 REMARK 620 3 HIS A 23 O 85.3 87.3 REMARK 620 4 THR A 26 O 95.5 160.2 86.9 REMARK 620 5 HOH A2042 O 153.4 79.8 121.2 87.1 REMARK 620 6 HOH A2063 O 75.1 86.3 157.4 105.8 78.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 95 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 85 NE2 REMARK 620 2 HIS A 89 NE2 109.6 REMARK 620 3 HIS B 15 NE2 106.4 102.3 REMARK 620 4 ASP B 25 OD1 120.5 112.4 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 92 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 18 O REMARK 620 2 LYS B 21 O 101.1 REMARK 620 3 HIS B 23 O 84.8 92.4 REMARK 620 4 THR B 26 O 90.4 168.4 86.7 REMARK 620 5 HOH B2055 O 78.9 84.2 162.3 100.0 REMARK 620 6 HOH B2108 O 174.3 84.6 94.5 84.0 102.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 92 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER C 18 O REMARK 620 2 LYS C 21 O 98.5 REMARK 620 3 HIS C 23 O 88.2 88.3 REMARK 620 4 THR C 26 O 96.6 164.5 88.9 REMARK 620 5 HOH C2051 O 76.5 79.7 158.8 107.3 REMARK 620 6 HOH C2092 O 177.7 80.1 93.7 84.9 101.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 95 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 15 NE2 REMARK 620 2 ASP C 25 OD1 100.2 REMARK 620 3 HIS D 85 NE2 107.0 124.1 REMARK 620 4 HIS D 89 NE2 106.0 110.6 107.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 95 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 85 NE2 REMARK 620 2 HIS C 89 NE2 105.6 REMARK 620 3 HIS D 15 NE2 111.3 113.7 REMARK 620 4 ASP D 25 OD1 121.3 106.0 99.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 92 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER D 18 O REMARK 620 2 LYS D 21 O 100.5 REMARK 620 3 HIS D 23 O 80.4 88.0 REMARK 620 4 THR D 26 O 93.4 165.9 92.0 REMARK 620 5 HOH D2057 O 75.7 78.9 149.9 107.3 REMARK 620 6 HOH D2110 O 177.4 78.3 97.2 87.7 106.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 92 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 95 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 92 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 95 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA C 92 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 95 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT C 1092 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA D 92 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 95 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WCB RELATED DB: PDB REMARK 900 S100A12 COMPLEX WITH ZINC IN THE ABSENCE OF CALCIUM REMARK 900 RELATED ID: 1GQM RELATED DB: PDB REMARK 900 THE STRUCTURE OF S100A12 IN A HEXAMERIC FORM AND ITS PROPOSED ROLE REMARK 900 IN RECEPTOR SIGNALLING REMARK 900 RELATED ID: 2WCF RELATED DB: PDB REMARK 900 CALCIUM-FREE S100A12 REMARK 900 RELATED ID: 1ODB RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF HUMAN S100A12 - COPPER COMPLEX REMARK 900 RELATED ID: 1E8A RELATED DB: PDB REMARK 900 THE THREE-DIMENSIONAL STRUCTURE OF HUMAN S100A12 REMARK 900 RELATED ID: 2WCE RELATED DB: PDB REMARK 900 CALCIUM-FREE S100A12 REMARK 999 REMARK 999 SEQUENCE REMARK 999 EXTRA FOUR RESIDUES AT N TERMINUS MGGS FOR CHAINS A,B,C,D DBREF 2WC8 A -3 0 PDB 2WC8 2WC8 -3 0 DBREF 2WC8 A 1 91 UNP P80511 S10AC_HUMAN 2 92 DBREF 2WC8 B -3 0 PDB 2WC8 2WC8 -3 0 DBREF 2WC8 B 1 91 UNP P80511 S10AC_HUMAN 2 92 DBREF 2WC8 C -3 0 PDB 2WC8 2WC8 -3 0 DBREF 2WC8 C 1 91 UNP P80511 S10AC_HUMAN 2 92 DBREF 2WC8 D -3 0 PDB 2WC8 2WC8 -3 0 DBREF 2WC8 D 1 91 UNP P80511 S10AC_HUMAN 2 92 SEQRES 1 A 95 MET GLY GLY SER THR LYS LEU GLU GLU HIS LEU GLU GLY SEQRES 2 A 95 ILE VAL ASN ILE PHE HIS GLN TYR SER VAL ARG LYS GLY SEQRES 3 A 95 HIS PHE ASP THR LEU SER LYS GLY GLU LEU LYS GLN LEU SEQRES 4 A 95 LEU THR LYS GLU LEU ALA ASN THR ILE LYS ASN ILE LYS SEQRES 5 A 95 ASP LYS ALA VAL ILE ASP GLU ILE PHE GLN GLY LEU ASP SEQRES 6 A 95 ALA ASN GLN ASP GLU GLN VAL ASP PHE GLN GLU PHE ILE SEQRES 7 A 95 SER LEU VAL ALA ILE ALA LEU LYS ALA ALA HIS TYR HIS SEQRES 8 A 95 THR HIS LYS GLU SEQRES 1 B 95 MET GLY GLY SER THR LYS LEU GLU GLU HIS LEU GLU GLY SEQRES 2 B 95 ILE VAL ASN ILE PHE HIS GLN TYR SER VAL ARG LYS GLY SEQRES 3 B 95 HIS PHE ASP THR LEU SER LYS GLY GLU LEU LYS GLN LEU SEQRES 4 B 95 LEU THR LYS GLU LEU ALA ASN THR ILE LYS ASN ILE LYS SEQRES 5 B 95 ASP LYS ALA VAL ILE ASP GLU ILE PHE GLN GLY LEU ASP SEQRES 6 B 95 ALA ASN GLN ASP GLU GLN VAL ASP PHE GLN GLU PHE ILE SEQRES 7 B 95 SER LEU VAL ALA ILE ALA LEU LYS ALA ALA HIS TYR HIS SEQRES 8 B 95 THR HIS LYS GLU SEQRES 1 C 95 MET GLY GLY SER THR LYS LEU GLU GLU HIS LEU GLU GLY SEQRES 2 C 95 ILE VAL ASN ILE PHE HIS GLN TYR SER VAL ARG LYS GLY SEQRES 3 C 95 HIS PHE ASP THR LEU SER LYS GLY GLU LEU LYS GLN LEU SEQRES 4 C 95 LEU THR LYS GLU LEU ALA ASN THR ILE LYS ASN ILE LYS SEQRES 5 C 95 ASP LYS ALA VAL ILE ASP GLU ILE PHE GLN GLY LEU ASP SEQRES 6 C 95 ALA ASN GLN ASP GLU GLN VAL ASP PHE GLN GLU PHE ILE SEQRES 7 C 95 SER LEU VAL ALA ILE ALA LEU LYS ALA ALA HIS TYR HIS SEQRES 8 C 95 THR HIS LYS GLU SEQRES 1 D 95 MET GLY GLY SER THR LYS LEU GLU GLU HIS LEU GLU GLY SEQRES 2 D 95 ILE VAL ASN ILE PHE HIS GLN TYR SER VAL ARG LYS GLY SEQRES 3 D 95 HIS PHE ASP THR LEU SER LYS GLY GLU LEU LYS GLN LEU SEQRES 4 D 95 LEU THR LYS GLU LEU ALA ASN THR ILE LYS ASN ILE LYS SEQRES 5 D 95 ASP LYS ALA VAL ILE ASP GLU ILE PHE GLN GLY LEU ASP SEQRES 6 D 95 ALA ASN GLN ASP GLU GLN VAL ASP PHE GLN GLU PHE ILE SEQRES 7 D 95 SER LEU VAL ALA ILE ALA LEU LYS ALA ALA HIS TYR HIS SEQRES 8 D 95 THR HIS LYS GLU HET NA A 92 1 HET ZN A 95 1 HET NA B 92 1 HET ZN B 95 1 HET NA C 92 1 HET ZN C 95 1 HET CIT C1092 13 HET NA D 92 1 HET ZN D 95 1 HETNAM NA SODIUM ION HETNAM ZN ZINC ION HETNAM CIT CITRIC ACID FORMUL 5 NA 4(NA 1+) FORMUL 6 ZN 4(ZN 2+) FORMUL 11 CIT C6 H8 O7 FORMUL 14 HOH *509(H2 O) HELIX 1 1 THR A 1 VAL A 19 1 19 HELIX 2 2 SER A 28 LEU A 40 1 13 HELIX 3 3 LEU A 40 ILE A 47 1 8 HELIX 4 4 ASP A 49 GLN A 58 1 10 HELIX 5 5 PHE A 70 HIS A 89 1 20 HELIX 6 6 THR B 1 VAL B 19 1 19 HELIX 7 7 LYS B 29 LEU B 40 1 12 HELIX 8 8 ASN B 46 PHE B 57 1 12 HELIX 9 9 ASP B 69 HIS B 89 1 21 HELIX 10 10 THR C 1 VAL C 19 1 19 HELIX 11 11 LYS C 29 LEU C 40 1 12 HELIX 12 12 LEU C 40 ILE C 47 1 8 HELIX 13 13 ASP C 49 GLN C 58 1 10 HELIX 14 14 ASP C 69 HIS C 89 1 21 HELIX 15 15 THR D 1 VAL D 19 1 19 HELIX 16 16 LYS D 29 LEU D 40 1 12 HELIX 17 17 LEU D 40 ILE D 47 1 8 HELIX 18 18 ASP D 49 PHE D 57 1 9 HELIX 19 19 ASP D 69 HIS D 89 1 21 SHEET 1 AA 2 THR A 26 LEU A 27 0 SHEET 2 AA 2 VAL A 68 ASP A 69 -1 O VAL A 68 N LEU A 27 SHEET 1 BA 2 LEU B 27 SER B 28 0 SHEET 2 BA 2 GLN B 67 VAL B 68 -1 O VAL B 68 N LEU B 27 SHEET 1 CA 2 LEU C 27 SER C 28 0 SHEET 2 CA 2 GLN C 67 VAL C 68 -1 O VAL C 68 N LEU C 27 SHEET 1 DA 2 LEU D 27 SER D 28 0 SHEET 2 DA 2 GLN D 67 VAL D 68 -1 O VAL D 68 N LEU D 27 LINK NE2 HIS A 15 ZN ZN A 95 1555 1555 2.08 LINK O SER A 18 NA NA A 92 1555 1555 2.37 LINK O LYS A 21 NA NA A 92 1555 1555 2.32 LINK O HIS A 23 NA NA A 92 1555 1555 2.44 LINK OD1 ASP A 25 ZN ZN A 95 1555 1555 1.94 LINK O THR A 26 NA NA A 92 1555 1555 2.35 LINK NE2 HIS A 85 ZN ZN B 95 1555 1555 2.10 LINK NE2 HIS A 89 ZN ZN B 95 1555 1555 2.08 LINK NA NA A 92 O HOH A2042 1555 1555 2.30 LINK NA NA A 92 O HOH A2063 1555 1555 2.48 LINK ZN ZN A 95 NE2 HIS B 85 1555 1555 2.12 LINK ZN ZN A 95 NE2 HIS B 89 1555 1555 2.01 LINK NE2 HIS B 15 ZN ZN B 95 1555 1555 2.08 LINK O SER B 18 NA NA C 92 1555 1555 2.36 LINK O LYS B 21 NA NA C 92 1555 1555 2.19 LINK O HIS B 23 NA NA C 92 1555 1555 2.32 LINK OD1 ASP B 25 ZN ZN B 95 1555 1555 1.92 LINK O THR B 26 NA NA C 92 1555 1555 2.40 LINK NA NA B 92 O SER C 18 1555 1555 2.34 LINK NA NA B 92 O LYS C 21 1555 1555 2.42 LINK NA NA B 92 O HIS C 23 1555 1555 2.12 LINK NA NA B 92 O THR C 26 1555 1555 2.31 LINK NA NA B 92 O HOH C2051 1555 1555 2.58 LINK NA NA B 92 O HOH C2092 1555 1555 2.30 LINK O HOH B2055 NA NA C 92 1555 1555 2.39 LINK O HOH B2108 NA NA C 92 1555 1555 2.24 LINK NE2 HIS C 15 ZN ZN C 95 1555 1555 2.10 LINK OD1 ASP C 25 ZN ZN C 95 1555 1555 1.90 LINK NE2 HIS C 85 ZN ZN D 95 1555 1555 2.01 LINK NE2 HIS C 89 ZN ZN D 95 1555 1555 2.02 LINK ZN ZN C 95 NE2 HIS D 85 1555 1555 2.08 LINK ZN ZN C 95 NE2 HIS D 89 1555 1555 2.02 LINK NE2 HIS D 15 ZN ZN D 95 1555 1555 2.05 LINK O SER D 18 NA NA D 92 1555 1555 2.25 LINK O LYS D 21 NA NA D 92 1555 1555 2.39 LINK O HIS D 23 NA NA D 92 1555 1555 2.18 LINK OD1 ASP D 25 ZN ZN D 95 1555 1555 1.91 LINK O THR D 26 NA NA D 92 1555 1555 2.32 LINK NA NA D 92 O HOH D2057 1555 1555 2.50 LINK NA NA D 92 O HOH D2110 1555 1555 2.39 SITE 1 AC1 6 SER A 18 LYS A 21 HIS A 23 THR A 26 SITE 2 AC1 6 HOH A2042 HOH A2063 SITE 1 AC2 4 HIS A 15 ASP A 25 HIS B 85 HIS B 89 SITE 1 AC3 6 SER C 18 LYS C 21 HIS C 23 THR C 26 SITE 2 AC3 6 HOH C2051 HOH C2092 SITE 1 AC4 4 HIS A 85 HIS A 89 HIS B 15 ASP B 25 SITE 1 AC5 6 SER B 18 LYS B 21 HIS B 23 THR B 26 SITE 2 AC5 6 HOH B2055 HOH B2108 SITE 1 AC6 4 HIS C 15 ASP C 25 HIS D 85 HIS D 89 SITE 1 AC7 9 ILE C 74 SER C 75 HOH C2115 HOH C2116 SITE 2 AC7 9 HOH C2117 HOH C2118 HOH C2119 LYS D 50 SITE 3 AC7 9 SER D 75 SITE 1 AC8 6 SER D 18 LYS D 21 HIS D 23 THR D 26 SITE 2 AC8 6 HOH D2057 HOH D2110 SITE 1 AC9 4 HIS C 85 HIS C 89 HIS D 15 ASP D 25 CRYST1 52.991 81.830 85.725 90.00 90.00 90.00 P 21 21 21 16 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 0.018871 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012220 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011665 0.00000