HEADER SIGNALING PROTEIN 26-OCT-01 1K96 TITLE CRYSTAL STRUCTURE OF CALCIUM BOUND HUMAN S100A6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: S100A6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CALCYCLIN, CACY; COMPND 5 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_STRAIN: BL21 (DE3) PLYS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PAED4 KEYWDS S100A6, CALCYCLIN, CALCIUM REGULATORY PROTEIN, CALCIUM BOUND, CACY, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.R.OTTERBEIN,R.DOMINGUEZ REVDAT 5 16-AUG-23 1K96 1 REMARK LINK REVDAT 4 13-JUL-11 1K96 1 VERSN REVDAT 3 24-FEB-09 1K96 1 VERSN REVDAT 2 01-APR-03 1K96 1 JRNL REVDAT 1 10-APR-02 1K96 0 JRNL AUTH L.R.OTTERBEIN,J.KORDOWSKA,C.WITTE-HOFFMANN,C.L.WANG, JRNL AUTH 2 R.DOMINGUEZ JRNL TITL CRYSTAL STRUCTURES OF S100A6 IN THE CA(2+)-FREE AND JRNL TITL 2 CA(2+)-BOUND STATES: THE CALCIUM SENSOR MECHANISM OF S100 JRNL TITL 3 PROTEINS REVEALED AT ATOMIC RESOLUTION. JRNL REF STRUCTURE V. 10 557 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 11937060 JRNL DOI 10.1016/S0969-2126(02)00740-2 REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14330 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 716 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 707 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1K96 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014716. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-SEP-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : CRYOGENICALLY COOLED SI(III) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14330 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.16600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PSORIASIN S100A7 (PDB # 1PSR) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 5000 MME, 30 MM TRIS-HCL, 8% REMARK 280 GLYCEROL, PH 7.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 22.59000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.61500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.59000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.61500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE TWO FOLD AXIS: REMARK 300 -X, Y, -Z 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 1 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 GLN A 66 -5.66 72.72 REMARK 500 LEU A 88 1.42 -69.77 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 91 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 20 O REMARK 620 2 GLU A 23 O 100.7 REMARK 620 3 ASP A 25 O 81.9 86.2 REMARK 620 4 THR A 28 O 92.8 158.0 78.6 REMARK 620 5 GLU A 33 OE2 79.2 76.2 151.1 123.8 REMARK 620 6 GLU A 33 OE1 96.8 119.3 154.0 75.5 51.1 REMARK 620 7 HOH A 98 O 173.6 81.0 92.1 83.7 107.2 87.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 92 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 61 OD1 REMARK 620 2 ASN A 63 OD1 82.8 REMARK 620 3 ASP A 65 OD1 79.4 78.4 REMARK 620 4 GLU A 67 O 85.5 151.6 74.0 REMARK 620 5 GLU A 72 OE1 117.2 128.3 148.1 80.0 REMARK 620 6 GLU A 72 OE2 95.6 79.8 158.1 127.2 52.7 REMARK 620 7 HOH A 120 O 156.3 87.5 77.5 93.1 85.7 103.9 REMARK 620 N 1 2 3 4 5 6 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 91 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 92 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 95 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K9P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CA2+ FREE(OR APO) S100A6 REMARK 900 RELATED ID: 1K8U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE CA2+ FREE HUMAN S100A6; CYS3MET MUTANT REMARK 900 (SELENOMETHIONINE DERIVATIVE) REMARK 900 RELATED ID: 1K9K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CA2+ BOUND S100A6 DBREF 1K96 A 1 90 UNP P06703 S10A6_HUMAN 1 90 SEQRES 1 A 90 MET ALA CYS PRO LEU ASP GLN ALA ILE GLY LEU LEU VAL SEQRES 2 A 90 ALA ILE PHE HIS LYS TYR SER GLY ARG GLU GLY ASP LYS SEQRES 3 A 90 HIS THR LEU SER LYS LYS GLU LEU LYS GLU LEU ILE GLN SEQRES 4 A 90 LYS GLU LEU THR ILE GLY SER LYS LEU GLN ASP ALA GLU SEQRES 5 A 90 ILE ALA ARG LEU MET GLU ASP LEU ASP ARG ASN LYS ASP SEQRES 6 A 90 GLN GLU VAL ASN PHE GLN GLU TYR VAL THR PHE LEU GLY SEQRES 7 A 90 ALA LEU ALA LEU ILE TYR ASN GLU ALA LEU LYS GLY HET CA A 91 1 HET CA A 92 1 HET BME A 95 4 HETNAM CA CALCIUM ION HETNAM BME BETA-MERCAPTOETHANOL FORMUL 2 CA 2(CA 2+) FORMUL 4 BME C2 H6 O S FORMUL 5 HOH *87(H2 O) HELIX 1 1 CYS A 3 GLY A 21 1 19 HELIX 2 2 SER A 30 LEU A 42 1 13 HELIX 3 3 LEU A 42 LEU A 48 1 7 HELIX 4 4 GLN A 49 ASP A 61 1 13 HELIX 5 5 ASN A 69 LEU A 88 1 20 LINK SG CYS A 3 S2 BME A 95 1555 1555 2.04 LINK O SER A 20 CA CA A 91 1555 1555 2.36 LINK O GLU A 23 CA CA A 91 1555 1555 2.39 LINK O ASP A 25 CA CA A 91 1555 1555 2.40 LINK O THR A 28 CA CA A 91 1555 1555 2.42 LINK OE2 GLU A 33 CA CA A 91 1555 1555 2.63 LINK OE1 GLU A 33 CA CA A 91 1555 1555 2.43 LINK OD1 ASP A 61 CA CA A 92 1555 1555 2.40 LINK OD1 ASN A 63 CA CA A 92 1555 1555 2.27 LINK OD1 ASP A 65 CA CA A 92 1555 1555 2.39 LINK O GLU A 67 CA CA A 92 1555 1555 2.23 LINK OE1 GLU A 72 CA CA A 92 1555 1555 2.37 LINK OE2 GLU A 72 CA CA A 92 1555 1555 2.56 LINK CA CA A 91 O HOH A 98 1555 1555 2.43 LINK CA CA A 92 O HOH A 120 1555 1555 2.86 SITE 1 AC1 6 SER A 20 GLU A 23 ASP A 25 THR A 28 SITE 2 AC1 6 GLU A 33 HOH A 98 SITE 1 AC2 6 ASP A 61 ASN A 63 ASP A 65 GLU A 67 SITE 2 AC2 6 GLU A 72 HOH A 120 SITE 1 AC3 4 CYS A 3 LYS A 40 GLU A 86 HOH A 149 CRYST1 45.180 39.230 48.110 90.00 110.44 90.00 C 1 2 1 4 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 0.022134 -0.000001 0.008248 0.00000 SCALE2 0.000000 0.025491 -0.000001 0.00000 SCALE3 0.000000 0.000000 0.022182 0.00000