HEADER IMMUNE SYSTEM 14-JUL-15 5CJ8 TITLE HUMAN OSTEOCLAST ASSOCIATED RECEPTOR (OSCAR) EXTRACELLULAR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: OSTEOCLAST-ASSOCIATED IMMUNOGLOBULIN-LIKE RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 31-215; COMPND 5 SYNONYM: HOSCAR,POLYMERIC IMMUNOGLOBULIN RECEPTOR 3,POLY-IG RECEPTOR COMPND 6 3; COMPND 7 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: OSCAR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IMMUNOGLOBULIN-LIKE, MONOMER, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR G.F.GAO,J.QI,Y.SHI,J.HAYWOOD REVDAT 3 08-NOV-23 5CJ8 1 JRNL REMARK REVDAT 2 10-FEB-16 5CJ8 1 JRNL REVDAT 1 20-JAN-16 5CJ8 0 JRNL AUTH J.HAYWOOD,J.QI,C.C.CHEN,G.LU,Y.LIU,J.YAN,Y.SHI,G.F.GAO JRNL TITL STRUCTURAL BASIS OF COLLAGEN RECOGNITION BY HUMAN JRNL TITL 2 OSTEOCLAST-ASSOCIATED RECEPTOR AND DESIGN OF JRNL TITL 3 OSTEOCLASTOGENESIS INHIBITORS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 1038 2016 JRNL REFN ESSN 1091-6490 JRNL PMID 26744311 JRNL DOI 10.1073/PNAS.1522572113 REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 10875 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 515 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 33.4408 - 3.1977 0.99 2683 155 0.1822 0.2090 REMARK 3 2 3.1977 - 2.5384 1.00 2649 123 0.2645 0.3106 REMARK 3 3 2.5384 - 2.2176 1.00 2652 133 0.2954 0.3490 REMARK 3 4 2.2176 - 2.0149 0.90 2376 104 0.2827 0.3448 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 46.09 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.200 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) : -0.26590 REMARK 3 B22 (A**2) : -3.36120 REMARK 3 B33 (A**2) : 3.62710 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.13030 REMARK 3 B23 (A**2) : 0.00000 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 : 0.009 1456 REMARK 3 ANGLE : 1.328 1993 REMARK 3 CHIRALITY : 0.090 214 REMARK 3 PLANARITY : 0.007 261 REMARK 3 DIHEDRAL : 15.548 532 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 5.4784 1.5404 22.5940 REMARK 3 T TENSOR REMARK 3 T11: 0.2107 T22: 0.2686 REMARK 3 T33: 0.2451 T12: 0.0021 REMARK 3 T13: -0.0194 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: -0.0807 L22: 0.7280 REMARK 3 L33: 0.8866 L12: -0.1086 REMARK 3 L13: -0.4849 L23: 0.3315 REMARK 3 S TENSOR REMARK 3 S11: 0.0226 S12: -0.0183 S13: 0.0102 REMARK 3 S21: -0.0012 S22: 0.0141 S23: -0.0338 REMARK 3 S31: 0.0921 S32: -0.0195 S33: -0.0000 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 5CJ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211734. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10875 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 STARTING MODEL: 1G0X, 1B6U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM FLUORIDE, 20% W/V REMARK 280 POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.23200 REMARK 290 SMTRY3 2 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 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 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 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 PRO A 142 REMARK 465 VAL A 143 REMARK 465 VAL A 144 REMARK 465 GLY A 145 REMARK 465 PRO A 146 REMARK 465 GLY A 147 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 LEU A 189 CG CD1 CD2 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 O ASN A 52 O HOH A 301 1.80 REMARK 500 O HOH A 363 O HOH A 364 1.87 REMARK 500 OG SER A 83 O HOH A 302 1.92 REMARK 500 C VAL A 82 O HOH A 302 1.93 REMARK 500 O VAL A 82 O HOH A 302 1.94 REMARK 500 SG CYS A 105 O HOH A 358 1.95 REMARK 500 N SER A 83 O HOH A 302 1.96 REMARK 500 O HOH A 301 O HOH A 347 2.00 REMARK 500 C ASN A 52 O HOH A 301 2.03 REMARK 500 O GLY A 141 O HOH A 303 2.10 REMARK 500 CA SER A 83 O HOH A 302 2.17 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 GLU A 93 44.17 37.05 REMARK 500 PRO A 182 45.33 -75.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CJB RELATED DB: PDB DBREF 5CJ8 A 35 219 UNP Q8IYS5 OSCAR_HUMAN 31 215 SEQRES 1 A 185 PRO LYS PRO TRP LEU GLY ALA GLN PRO ALA THR VAL VAL SEQRES 2 A 185 THR PRO GLY VAL ASN VAL THR LEU ARG CYS ARG ALA PRO SEQRES 3 A 185 GLN PRO ALA TRP ARG PHE GLY LEU PHE LYS PRO GLY GLU SEQRES 4 A 185 ILE ALA PRO LEU LEU PHE ARG ASP VAL SER SER GLU LEU SEQRES 5 A 185 ALA GLU PHE PHE LEU GLU GLU VAL THR PRO ALA GLN GLY SEQRES 6 A 185 GLY ILE TYR ARG CYS CYS TYR ARG ARG PRO ASP TRP GLY SEQRES 7 A 185 PRO GLY VAL TRP SER GLN PRO SER ASP VAL LEU GLU LEU SEQRES 8 A 185 LEU VAL THR GLU GLU LEU PRO ARG PRO SER LEU VAL ALA SEQRES 9 A 185 LEU PRO GLY PRO VAL VAL GLY PRO GLY ALA ASN VAL SER SEQRES 10 A 185 LEU ARG CYS ALA GLY ARG LEU ARG ASN MET SER PHE VAL SEQRES 11 A 185 LEU TYR ARG GLU GLY VAL ALA ALA PRO LEU GLN TYR ARG SEQRES 12 A 185 HIS SER ALA GLN PRO TRP ALA ASP PHE THR LEU LEU GLY SEQRES 13 A 185 ALA ARG ALA PRO GLY THR TYR SER CYS TYR TYR HIS THR SEQRES 14 A 185 PRO SER ALA PRO TYR VAL LEU SER GLN ARG SER GLU VAL SEQRES 15 A 185 LEU VAL ILE FORMUL 2 HOH *67(H2 O) HELIX 1 AA1 THR A 95 GLY A 99 5 5 HELIX 2 AA2 ALA A 191 ALA A 193 5 3 SHEET 1 AA1 5 TRP A 38 GLN A 42 0 SHEET 2 AA1 5 VAL A 53 PHE A 69 -1 O THR A 54 N GLN A 42 SHEET 3 AA1 5 GLY A 100 ARG A 107 -1 O ARG A 103 N PHE A 69 SHEET 4 AA1 5 LEU A 123 VAL A 127 -1 O LEU A 125 N GLY A 100 SHEET 5 AA1 5 VAL A 46 VAL A 47 1 N VAL A 47 O LEU A 126 SHEET 1 AA2 3 TRP A 38 GLN A 42 0 SHEET 2 AA2 3 VAL A 53 PHE A 69 -1 O THR A 54 N GLN A 42 SHEET 3 AA2 3 LEU A 78 LEU A 91 -1 O GLU A 85 N ALA A 59 SHEET 1 AA3 2 GLU A 130 LEU A 131 0 SHEET 2 AA3 2 LEU A 210 SER A 211 1 O LEU A 210 N LEU A 131 SHEET 1 AA4 3 SER A 135 ALA A 138 0 SHEET 2 AA4 3 ASN A 149 ALA A 155 -1 O ARG A 153 N VAL A 137 SHEET 3 AA4 3 TRP A 183 LEU A 189 -1 O PHE A 186 N LEU A 152 SHEET 1 AA5 4 GLN A 175 SER A 179 0 SHEET 2 AA5 4 MET A 161 ARG A 167 -1 N PHE A 163 O ARG A 177 SHEET 3 AA5 4 GLY A 195 HIS A 202 -1 O SER A 198 N TYR A 166 SHEET 4 AA5 4 LEU A 217 ILE A 219 -1 O ILE A 219 N GLY A 195 SSBOND 1 CYS A 57 CYS A 104 1555 1555 2.03 SSBOND 2 CYS A 154 CYS A 199 1555 1555 2.05 CISPEP 1 GLN A 42 PRO A 43 0 2.04 CISPEP 2 ALA A 206 PRO A 207 0 -8.79 CRYST1 27.215 46.464 66.980 90.00 93.25 90.00 P 1 21 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 0.036744 0.000000 0.002085 0.00000 SCALE2 0.000000 0.021522 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014954 0.00000