PDB Short entry for 2V53 HEADER CELL ADHESION 01-OCT-08 2V53 TITLE CRYSTAL STRUCTURE OF A SPARC-COLLAGEN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPARC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FS AND EC DOMAINS, RESIDUES 70-212,221-303; COMPND 5 SYNONYM: SECRETED PROTEIN ACIDIC AND RICH IN CYSTEINE, OSTEONECTIN, COMPND 6 ON, BASEMENT-MEMBRANE PROTEIN 40, BM-40; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: COLLAGEN ALPHA-1(III) CHAIN; COMPND 10 CHAIN: B, C, D; COMPND 11 FRAGMENT: RESIDUES 564-584; COMPND 12 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: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: 293-EBNA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PCEP-PU; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS GLYCOSYLATED PROTEIN, CELL ADHESION, GLYCOPROTEIN, IONIC CHANNEL, ION KEYWDS 2 TRANSPORT, COPPER, CALCIUM, SECRETED, COLLAGEN, TRANSPORT, BASEMENT KEYWDS 3 MEMBRANE, EXTRACELLULAR MATRIX EXPDTA X-RAY DIFFRACTION AUTHOR E.HOHENESTER,T.SASAKI,C.GIUDICI,R.W.FARNDALE,H.P.BACHINGER REVDAT 4 13-DEC-23 2V53 1 HETSYN REVDAT 3 29-JUL-20 2V53 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 09-DEC-08 2V53 1 VERSN JRNL REVDAT 1 25-NOV-08 2V53 0 JRNL AUTH E.HOHENESTER,T.SASAKI,C.GIUDICI,R.W.FARNDALE,H.P.BACHINGER JRNL TITL STRUCTURAL BASIS OF SEQUENCE-SPECIFIC COLLAGEN RECOGNITION JRNL TITL 2 BY SPARC. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 18273 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 19011090 JRNL DOI 10.1073/PNAS.0808452105 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.SASAKI,E.HOHENESTER,W.GOHRING,R.TIMPL REMARK 1 TITL CRYSTAL STRUCTURE AND MAPPING BY SITE-DIRECTED MUTAGENESIS REMARK 1 TITL 2 OF THE COLLAGEN-BINDING EPITOPE OF AN ACTIVATED FORM OF REMARK 1 TITL 3 BM-40,SPARC,OSTEONECTIN REMARK 1 REF EMBO J. V. 17 1625 1998 REMARK 1 REFN ISSN 0261-4189 REMARK 1 PMID 9501084 REMARK 1 DOI 10.1093/EMBOJ/17.6.1625 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9019 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.254 REMARK 3 FREE R VALUE : 0.320 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.530 REMARK 3 FREE R VALUE TEST SET COUNT : 950 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 19.8422 - 6.0711 1.00 1236 150 0.2229 0.2694 REMARK 3 2 6.0711 - 4.8418 1.00 1159 146 0.2424 0.3371 REMARK 3 3 4.8418 - 4.2366 1.00 1132 142 0.2187 0.3030 REMARK 3 4 4.2366 - 3.8523 1.00 1146 133 0.2566 0.3092 REMARK 3 5 3.8523 - 3.5779 1.00 1151 130 0.2842 0.3356 REMARK 3 6 3.5779 - 3.3681 1.00 1111 137 0.2757 0.3842 REMARK 3 7 3.3681 - 3.2001 1.00 1134 112 0.3094 0.4058 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.25 REMARK 3 B_SOL : 26.82 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.580 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 74.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 87.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.48950 REMARK 3 B22 (A**2) : 2.48950 REMARK 3 B33 (A**2) : -10.78310 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 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 : 0.000 2392 REMARK 3 ANGLE : 1.410 3275 REMARK 3 CHIRALITY : 0.070 355 REMARK 3 PLANARITY : 0.000 433 REMARK 3 DIHEDRAL : 23.500 859 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 54:85 OR RESSEQ 105:114) REMARK 3 ORIGIN FOR THE GROUP (A): 11.2295 -0.5784 41.1595 REMARK 3 T TENSOR REMARK 3 T11: 1.6696 T22: 0.6492 REMARK 3 T33: 1.0095 T12: -0.0007 REMARK 3 T13: 0.5717 T23: 0.1416 REMARK 3 L TENSOR REMARK 3 L11: 0.3477 L22: 0.0897 REMARK 3 L33: 0.1306 L12: 0.3664 REMARK 3 L13: 0.1203 L23: 0.0181 REMARK 3 S TENSOR REMARK 3 S11: 0.8126 S12: 0.0555 S13: 0.5640 REMARK 3 S21: -1.4577 S22: -0.0712 S23: -1.5319 REMARK 3 S31: -0.7007 S32: 1.3629 S33: 0.0019 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 86:104 OR RESSEQ 115:135 OR REMARK 3 RESSEQ 401:402) REMARK 3 ORIGIN FOR THE GROUP (A): 1.2085 14.9927 52.4997 REMARK 3 T TENSOR REMARK 3 T11: 0.9646 T22: 0.2914 REMARK 3 T33: 0.7461 T12: -0.0532 REMARK 3 T13: -0.3034 T23: 0.1781 REMARK 3 L TENSOR REMARK 3 L11: 4.5242 L22: 2.1885 REMARK 3 L33: 2.4664 L12: -1.4510 REMARK 3 L13: -3.4292 L23: 0.8747 REMARK 3 S TENSOR REMARK 3 S11: 0.1266 S12: -0.8493 S13: -0.2257 REMARK 3 S21: -2.2387 S22: 1.3084 S23: 1.4652 REMARK 3 S31: 0.4853 S32: 0.0792 S33: 0.3303 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 136:187 OR RESSEQ 206:285 OR REMARK 3 RESSEQ 301) REMARK 3 ORIGIN FOR THE GROUP (A): 14.5351 34.8188 45.7834 REMARK 3 T TENSOR REMARK 3 T11: 0.7424 T22: 0.3408 REMARK 3 T33: 0.6680 T12: -0.0849 REMARK 3 T13: 0.0643 T23: 0.1323 REMARK 3 L TENSOR REMARK 3 L11: 0.3610 L22: 2.5222 REMARK 3 L33: 0.9679 L12: 0.1785 REMARK 3 L13: 0.7234 L23: -0.7858 REMARK 3 S TENSOR REMARK 3 S11: -0.1245 S12: 0.2919 S13: 0.3433 REMARK 3 S21: -0.3791 S22: 0.1468 S23: 0.0317 REMARK 3 S31: -0.4203 S32: -0.2269 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B OR CHAIN C OR CHAIN D OR CHAIN Z REMARK 3 ORIGIN FOR THE GROUP (A): 24.2629 16.1195 54.1475 REMARK 3 T TENSOR REMARK 3 T11: 1.0191 T22: 0.6426 REMARK 3 T33: 0.5268 T12: 0.0640 REMARK 3 T13: 0.1750 T23: -0.1678 REMARK 3 L TENSOR REMARK 3 L11: 1.0561 L22: -0.3754 REMARK 3 L33: 1.1913 L12: 0.0711 REMARK 3 L13: 0.6410 L23: -0.2858 REMARK 3 S TENSOR REMARK 3 S11: 0.2148 S12: 0.4872 S13: 0.3098 REMARK 3 S21: 0.3994 S22: -0.4553 S23: -0.2217 REMARK 3 S31: 0.3936 S32: 0.0857 S33: -0.0001 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 2V53 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1290037708. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX10.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9046 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.30 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, AUTOSHARP REMARK 200 STARTING MODEL: PDB ENTRY 1NUB REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 44.89500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.89500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 63.55000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.89500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.89500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 63.55000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.89500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.89500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 63.55000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.89500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.89500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.55000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 7810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 ALA A 49 REMARK 465 PRO A 50 REMARK 465 LEU A 51 REMARK 465 ALA A 52 REMARK 465 ASN A 53 REMARK 465 ARG A 188 REMARK 465 LEU A 189 REMARK 465 GLU A 190 REMARK 465 ALA A 191 REMARK 465 GLY A 192 REMARK 465 ASP A 193 REMARK 465 HIS A 194 REMARK 465 PRO A 195 REMARK 465 GLU A 204 REMARK 465 LYS A 205 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 PRO A 54 CG CD REMARK 470 GLN A 56 CG CD OE1 NE2 REMARK 470 ASN A 57 CG OD1 ND2 REMARK 470 HIS A 59 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 GLU A 70 CG CD OE1 OE2 REMARK 470 THR A 73 OG1 CG2 REMARK 470 GLN A 79 CG CD OE1 NE2 REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 LYS A 119 CG CD CE NZ REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 HIS A 122 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 123 CG CD CE NZ REMARK 470 LYS A 155 CG CD CE NZ REMARK 470 LYS A 174 CG CD CE NZ REMARK 470 ARG A 178 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 180 CG CD CE NZ REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 GLU A 184 CG CD OE1 OE2 REMARK 470 GLU A 186 CG CD OE1 OE2 REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 LYS A 262 CG CD CE NZ REMARK 470 LYS A 276 CG CD CE NZ REMARK 470 LYS A 278 CG CD CE NZ REMARK 470 LYS A 282 CG CD CE NZ REMARK 470 ILE A 286 CA C O CB CG1 CG2 CD1 REMARK 470 ARG B 15 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 27 CG CD CE NZ REMARK 470 LYS C 27 CG CD CE NZ REMARK 470 LYS D 27 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 54 N - CA - CB ANGL. DEV. = 7.2 DEGREES REMARK 500 PRO B 5 C - N - CA ANGL. DEV. = 9.1 DEGREES 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 GLN A 56 -37.45 -32.75 REMARK 500 LYS A 61 162.37 -49.88 REMARK 500 GLU A 70 -4.38 -59.64 REMARK 500 ASN A 97 -36.27 -35.12 REMARK 500 PHE A 109 -70.86 -63.63 REMARK 500 THR A 114 45.44 -80.40 REMARK 500 GLU A 116 142.66 165.25 REMARK 500 TYR A 128 160.77 177.85 REMARK 500 GLU A 145 1.74 -46.89 REMARK 500 THR A 160 2.66 -64.92 REMARK 500 TYR A 162 -38.51 -37.24 REMARK 500 ASP A 167 64.64 93.22 REMARK 500 ASN A 168 23.74 44.20 REMARK 500 THR A 172 -163.63 -57.77 REMARK 500 LYS A 176 -18.61 -43.03 REMARK 500 HIS A 183 -84.63 -59.65 REMARK 500 GLU A 184 85.28 -30.88 REMARK 500 ASN A 185 86.74 -158.22 REMARK 500 GLU A 186 33.56 -94.12 REMARK 500 TYR A 207 -34.11 -32.11 REMARK 500 ASN A 208 25.03 -71.20 REMARK 500 MET A 209 -61.65 -131.32 REMARK 500 TYR A 210 -35.57 -39.22 REMARK 500 PRO A 213 -77.86 -30.74 REMARK 500 LEU A 221 -82.99 -79.16 REMARK 500 ASP A 222 100.82 -33.55 REMARK 500 GLN A 223 -3.35 -158.49 REMARK 500 ASP A 227 -7.27 -149.47 REMARK 500 ALA A 236 -64.45 -21.77 REMARK 500 PRO A 237 -6.24 -58.24 REMARK 500 PRO A 241 0.46 -69.35 REMARK 500 GLU A 246 82.67 -155.75 REMARK 500 THR A 255 33.28 -95.15 REMARK 500 ASP A 257 77.55 -66.48 REMARK 500 LYS A 262 16.91 53.58 REMARK 500 ILE A 280 90.95 -65.69 REMARK 500 LYS A 282 15.34 -60.17 REMARK 500 PRO B 5 172.97 -38.87 REMARK 500 MET B 21 165.74 -48.30 REMARK 500 ALA B 32 151.31 -33.30 REMARK 500 VAL C 20 157.39 -41.29 REMARK 500 HYP D 6 157.20 -45.18 REMARK 500 PRO D 26 -176.04 -49.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 4-HYDROXYPROLINE (HYP): 2R,4R-HYDROXYPROLINE REMARK 600 N-ACETYLGLUCOSAMINE (NAG): A401 IS N-LINKED TO ASPARAGINE REMARK 600 A99, A402 IS 1-4 LINKED TO A401 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 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 222 OD1 REMARK 620 2 PRO A 225 O 80.3 REMARK 620 3 ASP A 227 OD2 80.2 75.5 REMARK 620 4 TYR A 229 O 85.6 146.9 72.6 REMARK 620 5 GLU A 234 OE1 113.3 149.0 132.6 64.0 REMARK 620 6 GLU A 234 OE2 91.0 106.5 170.6 103.6 48.4 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NUB RELATED DB: PDB REMARK 900 HELIX C DELETION MUTANT OF BM-40 FS-EC DOMAIN PAIR REMARK 900 RELATED ID: 1BMO RELATED DB: PDB REMARK 900 BM-40, FS/EC DOMAIN PAIR REMARK 900 RELATED ID: 1SRA RELATED DB: PDB REMARK 900 STRUCTURE OF A NOVEL EXTRACELLULAR CA2+-BINDING MODULE IN BM- REMARK 900 40(SLASH)SPARC(SLASH)OSTEONECTIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 REGARDING CHAIN A: VECTOR-DERIVED APLA AT N-TERMINUS, REMARK 999 196-203 DELETED REMARK 999 REGARDING CHAINS B, C AND D: PEPTIDE CORRESPONDS TO REMARK 999 564-584 OF HUMAN COLLAGEN ALPHA1(III) CHAIN, FLANKED REMARK 999 BY GPOGPO AT N-TERMINUS AND GPOGAO AT C-TERMINUS REMARK 999 (O IS 4-HYDROXYPROLINE) DBREF 2V53 A 49 52 PDB 2V53 2V53 49 52 DBREF 2V53 A 53 195 UNP P09486 SPRC_HUMAN 70 212 DBREF 2V53 A 204 286 UNP P09486 SPRC_HUMAN 221 303 DBREF 2V53 B 1 6 PDB 2V53 2V53 1 6 DBREF 2V53 B 7 27 UNP P02461 CO3A1_HUMAN 564 584 DBREF 2V53 B 28 33 PDB 2V53 2V53 28 33 DBREF 2V53 C 1 6 PDB 2V53 2V53 1 6 DBREF 2V53 C 7 27 UNP P02461 CO3A1_HUMAN 564 584 DBREF 2V53 C 28 33 PDB 2V53 2V53 28 33 DBREF 2V53 D 1 6 PDB 2V53 2V53 1 6 DBREF 2V53 D 7 27 UNP P02461 CO3A1_HUMAN 564 584 DBREF 2V53 D 28 33 PDB 2V53 2V53 28 33 SEQRES 1 A 230 ALA PRO LEU ALA ASN PRO CYS GLN ASN HIS HIS CYS LYS SEQRES 2 A 230 HIS GLY LYS VAL CYS GLU LEU ASP GLU ASN ASN THR PRO SEQRES 3 A 230 MET CYS VAL CYS GLN ASP PRO THR SER CYS PRO ALA PRO SEQRES 4 A 230 ILE GLY GLU PHE GLU LYS VAL CYS SER ASN ASP ASN LYS SEQRES 5 A 230 THR PHE ASP SER SER CYS HIS PHE PHE ALA THR LYS CYS SEQRES 6 A 230 THR LEU GLU GLY THR LYS LYS GLY HIS LYS LEU HIS LEU SEQRES 7 A 230 ASP TYR ILE GLY PRO CYS LYS TYR ILE PRO PRO CYS LEU SEQRES 8 A 230 ASP SER GLU LEU THR GLU PHE PRO LEU ARG MET ARG ASP SEQRES 9 A 230 TRP LEU LYS ASN VAL LEU VAL THR LEU TYR GLU ARG ASP SEQRES 10 A 230 GLU ASP ASN ASN LEU LEU THR GLU LYS GLN LYS LEU ARG SEQRES 11 A 230 VAL LYS LYS ILE HIS GLU ASN GLU LYS ARG LEU GLU ALA SEQRES 12 A 230 GLY ASP HIS PRO GLU LYS ASN TYR ASN MET TYR ILE PHE SEQRES 13 A 230 PRO VAL HIS TRP GLN PHE GLY GLN LEU ASP GLN HIS PRO SEQRES 14 A 230 ILE ASP GLY TYR LEU SER HIS THR GLU LEU ALA PRO LEU SEQRES 15 A 230 ARG ALA PRO LEU ILE PRO MET GLU HIS CYS THR THR ARG SEQRES 16 A 230 PHE PHE GLU THR CYS ASP LEU ASP ASN ASP LYS TYR ILE SEQRES 17 A 230 ALA LEU ASP GLU TRP ALA GLY CYS PHE GLY ILE LYS GLN SEQRES 18 A 230 LYS ASP ILE ASP LYS ASP LEU VAL ILE SEQRES 1 B 33 GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO SER GLY SEQRES 2 B 33 PRO ARG GLY GLN HYP GLY VAL MET GLY PHE HYP GLY PRO SEQRES 3 B 33 LYS GLY PRO HYP GLY ALA HYP SEQRES 1 C 33 GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO SER GLY SEQRES 2 C 33 PRO ARG GLY GLN HYP GLY VAL MET GLY PHE HYP GLY PRO SEQRES 3 C 33 LYS GLY PRO HYP GLY ALA HYP SEQRES 1 D 33 GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO SER GLY SEQRES 2 D 33 PRO ARG GLY GLN HYP GLY VAL MET GLY PHE HYP GLY PRO SEQRES 3 D 33 LYS GLY PRO HYP GLY ALA HYP MODRES 2V53 ASN A 99 ASN GLYCOSYLATION SITE MODRES 2V53 HYP B 3 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP B 6 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP B 9 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP B 18 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP B 24 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP B 30 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP B 33 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP C 3 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP C 6 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP C 9 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP C 18 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP C 24 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP C 30 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP C 33 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP D 3 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP D 6 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP D 9 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP D 18 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP D 24 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP D 30 PRO 4-HYDROXYPROLINE MODRES 2V53 HYP D 33 PRO 4-HYDROXYPROLINE HET HYP B 3 8 HET HYP B 6 8 HET HYP B 9 8 HET HYP B 18 8 HET HYP B 24 8 HET HYP B 30 8 HET HYP B 33 8 HET HYP C 3 8 HET HYP C 6 8 HET HYP C 9 8 HET HYP C 18 8 HET HYP C 24 8 HET HYP C 30 8 HET HYP C 33 8 HET HYP D 3 8 HET HYP D 6 8 HET HYP D 9 8 HET HYP D 18 8 HET HYP D 24 8 HET HYP D 30 8 HET HYP D 33 8 HET NAG E 1 14 HET NAG E 2 14 HET CA A 301 1 HET SO4 D 401 5 HETNAM HYP 4-HYDROXYPROLINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETSYN HYP HYDROXYPROLINE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 HYP 21(C5 H9 N O3) FORMUL 5 NAG 2(C8 H15 N O6) FORMUL 6 CA CA 2+ FORMUL 7 SO4 O4 S 2- HELIX 1 1 ASP A 80 CYS A 84 5 5 HELIX 2 2 SER A 104 THR A 114 1 11 HELIX 3 3 LEU A 139 GLU A 145 1 7 HELIX 4 4 PHE A 146 GLU A 163 1 18 HELIX 5 5 THR A 172 GLU A 184 1 13 HELIX 6 6 TYR A 210 ASP A 222 1 13 HELIX 7 7 SER A 231 ALA A 240 1 10 HELIX 8 8 LEU A 242 GLU A 246 5 5 HELIX 9 9 HIS A 247 THR A 255 1 9 HELIX 10 10 LEU A 266 PHE A 273 1 8 SHEET 1 AA 2 LYS A 64 LEU A 68 0 SHEET 2 AA 2 PRO A 74 CYS A 78 -1 O MET A 75 N GLU A 67 SHEET 1 AB 2 VAL A 94 CYS A 95 0 SHEET 2 AB 2 TYR A 128 ILE A 129 -1 O TYR A 128 N CYS A 95 SHEET 1 AC 2 TYR A 229 LEU A 230 0 SHEET 2 AC 2 ILE A 264 ALA A 265 -1 O ILE A 264 N LEU A 230 SSBOND 1 CYS A 55 CYS A 66 1555 1555 2.04 SSBOND 2 CYS A 60 CYS A 76 1555 1555 2.03 SSBOND 3 CYS A 78 CYS A 113 1555 1555 2.04 SSBOND 4 CYS A 84 CYS A 106 1555 1555 2.04 SSBOND 5 CYS A 95 CYS A 132 1555 1555 2.02 SSBOND 6 CYS A 138 CYS A 248 1555 1555 2.04 SSBOND 7 CYS A 256 CYS A 272 1555 1555 2.03 LINK ND2 ASN A 99 C1 NAG E 1 1555 1555 1.44 LINK C PRO B 2 N HYP B 3 1555 1555 1.33 LINK C HYP B 3 N GLY B 4 1555 1555 1.34 LINK C PRO B 5 N HYP B 6 1555 1555 1.33 LINK C HYP B 6 N GLY B 7 1555 1555 1.33 LINK C PRO B 8 N HYP B 9 1555 1555 1.33 LINK C HYP B 9 N GLY B 10 1555 1555 1.33 LINK C GLN B 17 N HYP B 18 1555 1555 1.33 LINK C HYP B 18 N GLY B 19 1555 1555 1.32 LINK C PHE B 23 N HYP B 24 1555 1555 1.33 LINK C HYP B 24 N GLY B 25 1555 1555 1.32 LINK C PRO B 29 N HYP B 30 1555 1555 1.33 LINK C HYP B 30 N GLY B 31 1555 1555 1.33 LINK C ALA B 32 N HYP B 33 1555 1555 1.33 LINK C PRO C 2 N HYP C 3 1555 1555 1.33 LINK C HYP C 3 N GLY C 4 1555 1555 1.33 LINK C PRO C 5 N HYP C 6 1555 1555 1.33 LINK C HYP C 6 N GLY C 7 1555 1555 1.33 LINK C PRO C 8 N HYP C 9 1555 1555 1.33 LINK C HYP C 9 N GLY C 10 1555 1555 1.33 LINK C GLN C 17 N HYP C 18 1555 1555 1.33 LINK C HYP C 18 N GLY C 19 1555 1555 1.32 LINK C PHE C 23 N HYP C 24 1555 1555 1.33 LINK C HYP C 24 N GLY C 25 1555 1555 1.32 LINK C PRO C 29 N HYP C 30 1555 1555 1.33 LINK C HYP C 30 N GLY C 31 1555 1555 1.33 LINK C ALA C 32 N HYP C 33 1555 1555 1.33 LINK C PRO D 2 N HYP D 3 1555 1555 1.33 LINK C HYP D 3 N GLY D 4 1555 1555 1.33 LINK C PRO D 5 N HYP D 6 1555 1555 1.33 LINK C HYP D 6 N GLY D 7 1555 1555 1.33 LINK C PRO D 8 N HYP D 9 1555 1555 1.33 LINK C HYP D 9 N GLY D 10 1555 1555 1.33 LINK C GLN D 17 N HYP D 18 1555 1555 1.33 LINK C HYP D 18 N GLY D 19 1555 1555 1.32 LINK C PHE D 23 N HYP D 24 1555 1555 1.32 LINK C HYP D 24 N GLY D 25 1555 1555 1.33 LINK C PRO D 29 N HYP D 30 1555 1555 1.33 LINK C HYP D 30 N GLY D 31 1555 1555 1.33 LINK C ALA D 32 N HYP D 33 1555 1555 1.33 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.44 LINK OD1 ASP A 222 CA CA A 301 1555 1555 2.58 LINK O PRO A 225 CA CA A 301 1555 1555 2.59 LINK OD2 ASP A 227 CA CA A 301 1555 1555 2.63 LINK O TYR A 229 CA CA A 301 1555 1555 2.69 LINK OE1 GLU A 234 CA CA A 301 1555 1555 2.62 LINK OE2 GLU A 234 CA CA A 301 1555 1555 2.75 CISPEP 1 HIS A 224 PRO A 225 0 -1.95 CRYST1 89.790 89.790 127.100 90.00 90.00 90.00 P 42 21 2 24 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 0.011137 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007868 0.00000