HEADER PROTEIN BINDING 31-AUG-10 3OP8 TITLE CRYSTAL STRUCTURE OF THE DOMAIN V FROM BETA2-GLYCOPROTEIN I COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-2-GLYCOPROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DOMAIN V (UNP RESIDUES 263-345); COMPND 5 SYNONYM: BETA-2-GLYCOPROTEIN I, BETA(2)GPI, B2GPI, APOLIPOPROTEIN H, COMPND 6 APO-H, ACTIVATED PROTEIN C-BINDING PROTEIN, APC INHIBITOR, COMPND 7 ANTICARDIOLIPIN COFACTOR; 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 GENE: APOH, B2GPI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS SUSHI, ANTIPHOSPHOLIPID SYNDROME, ANIONIC PHOSPHOLIPIDS BINDING, KEYWDS 2 LIPOPROTEIN RECEPTORS BINDING, BLOOD PLASMA, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.KOLYADA,C.-J.LEE,A.DE BIASIO,N.BEGLOVA REVDAT 2 30-MAR-11 3OP8 1 REMARK REVDAT 1 05-JAN-11 3OP8 0 JRNL AUTH A.KOLYADA,C.J.LEE,A.DE BIASIO,N.BEGLOVA JRNL TITL A NOVEL DIMERIC INHIBITOR TARGETING BETA2GPI IN JRNL TITL 2 BETA2GPI/ANTIBODY COMPLEXES IMPLICATED IN ANTIPHOSPHOLIPID JRNL TITL 3 SYNDROME. JRNL REF PLOS ONE V. 5 E1534 2010 JRNL REFN ESSN 1932-6203 JRNL PMID 21179511 JRNL DOI 10.1371/JOURNAL.PONE.0015345 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.2_432) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 12598 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 632 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.0073 - 3.2484 0.93 2390 148 0.1744 0.1964 REMARK 3 2 3.2484 - 2.5785 0.94 2460 113 0.1841 0.2327 REMARK 3 3 2.5785 - 2.2526 0.94 2406 114 0.1916 0.2530 REMARK 3 4 2.2526 - 2.0467 0.93 2419 119 0.1724 0.2239 REMARK 3 5 2.0467 - 1.9000 0.90 2291 138 0.1846 0.2389 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.77 REMARK 3 K_SOL : 0.48 REMARK 3 B_SOL : 48.36 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.016 1388 REMARK 3 ANGLE : 1.534 1850 REMARK 3 CHIRALITY : 0.106 195 REMARK 3 PLANARITY : 0.007 230 REMARK 3 DIHEDRAL : 13.165 522 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3OP8 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-10. REMARK 100 THE RCSB ID CODE IS RCSB061400. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0750 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17881 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.26700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M (NH4)2SO4, BIS-TRIS 0.1M, PEG REMARK 280 1500 40 %, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ASP A 298 68.99 32.02 REMARK 500 GLU B 265 -65.90 -97.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C1Z RELATED DB: PDB REMARK 900 RELATED ID: 1QUB RELATED DB: PDB DBREF 3OP8 A 244 326 UNP P02749 APOH_HUMAN 263 345 DBREF 3OP8 B 244 326 UNP P02749 APOH_HUMAN 263 345 SEQADV 3OP8 GLY A 243 UNP P02749 EXPRESSION TAG SEQADV 3OP8 LEU A 247 UNP P02749 VAL 266 CONFLICT SEQADV 3OP8 ALA A 327 UNP P02749 EXPRESSION TAG SEQADV 3OP8 GLY B 243 UNP P02749 EXPRESSION TAG SEQADV 3OP8 LEU B 247 UNP P02749 VAL 266 CONFLICT SEQADV 3OP8 ALA B 327 UNP P02749 EXPRESSION TAG SEQRES 1 A 85 GLY SER CYS LYS LEU PRO VAL LYS LYS ALA THR VAL VAL SEQRES 2 A 85 TYR GLN GLY GLU ARG VAL LYS ILE GLN GLU LYS PHE LYS SEQRES 3 A 85 ASN GLY MET LEU HIS GLY ASP LYS VAL SER PHE PHE CYS SEQRES 4 A 85 LYS ASN LYS GLU LYS LYS CYS SER TYR THR GLU ASP ALA SEQRES 5 A 85 GLN CYS ILE ASP GLY THR ILE GLU VAL PRO LYS CYS PHE SEQRES 6 A 85 LYS GLU HIS SER SER LEU ALA PHE TRP LYS THR ASP ALA SEQRES 7 A 85 SER ASP VAL LYS PRO CYS ALA SEQRES 1 B 85 GLY SER CYS LYS LEU PRO VAL LYS LYS ALA THR VAL VAL SEQRES 2 B 85 TYR GLN GLY GLU ARG VAL LYS ILE GLN GLU LYS PHE LYS SEQRES 3 B 85 ASN GLY MET LEU HIS GLY ASP LYS VAL SER PHE PHE CYS SEQRES 4 B 85 LYS ASN LYS GLU LYS LYS CYS SER TYR THR GLU ASP ALA SEQRES 5 B 85 GLN CYS ILE ASP GLY THR ILE GLU VAL PRO LYS CYS PHE SEQRES 6 B 85 LYS GLU HIS SER SER LEU ALA PHE TRP LYS THR ASP ALA SEQRES 7 B 85 SER ASP VAL LYS PRO CYS ALA HET SO4 A 3 5 HET SO4 A 2 5 HET SO4 B 1 5 HET SO4 B 4 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 HOH *110(H2 O) HELIX 1 1 ILE A 263 PHE A 267 1 5 HELIX 2 2 ASP A 319 VAL A 323 5 5 HELIX 3 3 ILE B 263 PHE B 267 1 5 HELIX 4 4 ASP B 319 VAL B 323 5 5 SHEET 1 A 5 GLU A 259 LYS A 262 0 SHEET 2 A 5 THR A 253 TYR A 256 -1 N TYR A 256 O GLU A 259 SHEET 3 A 5 LYS A 276 ASN A 283 -1 O SER A 278 N VAL A 255 SHEET 4 A 5 CYS A 288 ILE A 297 -1 O CYS A 288 N ASN A 283 SHEET 5 A 5 THR A 300 ILE A 301 -1 O THR A 300 N ILE A 297 SHEET 1 B 2 SER B 244 CYS B 245 0 SHEET 2 B 2 MET B 271 LEU B 272 -1 O MET B 271 N CYS B 245 SHEET 1 C 5 GLU B 259 LYS B 262 0 SHEET 2 C 5 THR B 253 TYR B 256 -1 N TYR B 256 O GLU B 259 SHEET 3 C 5 LYS B 276 ASN B 283 -1 O SER B 278 N VAL B 255 SHEET 4 C 5 CYS B 288 ILE B 297 -1 O TYR B 290 N CYS B 281 SHEET 5 C 5 THR B 300 ILE B 301 -1 O THR B 300 N ILE B 297 SSBOND 1 CYS A 245 CYS A 296 1555 1555 2.02 SSBOND 2 CYS A 281 CYS A 306 1555 1555 2.06 SSBOND 3 CYS A 288 CYS A 326 1555 1555 2.06 SSBOND 4 CYS B 245 CYS B 296 1555 1555 2.02 SSBOND 5 CYS B 281 CYS B 306 1555 1555 2.08 SSBOND 6 CYS B 288 CYS B 326 1555 1555 2.07 SITE 1 AC1 4 HOH A 55 LYS A 282 LYS A 284 LYS A 308 SITE 1 AC2 5 HOH A 10 LYS A 251 PRO A 304 LYS A 305 SITE 2 AC2 5 SER A 312 SITE 1 AC3 5 HOH B 29 LYS B 251 PRO B 304 LYS B 305 SITE 2 AC3 5 SER B 312 SITE 1 AC4 3 HOH B 106 LYS B 282 LYS B 317 CRYST1 24.290 38.090 49.510 93.83 102.65 90.09 P 1 2 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 0.041169 0.000065 0.009267 0.00000 SCALE2 0.000000 0.026254 0.001811 0.00000 SCALE3 0.000000 0.000000 0.020750 0.00000