HEADER CELL ADHESION 17-MAY-02 1LSL TITLE CRYSTAL STRUCTURE OF THE THROMBOSPONDIN-1 TYPE 1 REPEATS CAVEAT 1LSL FUC A 1489 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBOSPONDIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TSP TYPE 1 REPEATS 2 AND 3 (RESIDUES 434-546); 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 GENE: THBS1; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FRUIT FLIES; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7215; SOURCE 9 EXPRESSION_SYSTEM_CELL: S2 CELLS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: EUKARYOTIC; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PMT-BIP-V5-HIS A KEYWDS TSP-1, TSR, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,M.DUQUETTE,J.LIU,Y.DONG,R.ZHANG,A.JOACHIMIAK,J.LAWLER,J.-H.WANG REVDAT 4 30-OCT-24 1LSL 1 HETSYN REVDAT 3 29-JUL-20 1LSL 1 CAVEAT COMPND REMARK HETNAM REVDAT 3 2 1 LINK SITE REVDAT 2 24-FEB-09 1LSL 1 VERSN REVDAT 1 18-DEC-02 1LSL 0 JRNL AUTH K.TAN,M.DUQUETTE,J.H.LIU,Y.DONG,R.ZHANG,A.JOACHIMIAK, JRNL AUTH 2 J.LAWLER,J.H.WANG JRNL TITL CRYSTAL STRUCTURE OF THE TSP-1 TYPE 1 REPEATS: A NOVEL JRNL TITL 2 LAYERED FOLD AND ITS BIOLOGICAL IMPLICATION. JRNL REF J.CELL BIOL. V. 159 373 2002 JRNL REFN ISSN 0021-9525 JRNL PMID 12391027 JRNL DOI 10.1083/JCB.200206062 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15123 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1533 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1545 REMARK 3 BIN R VALUE (WORKING SET) : 0.4390 REMARK 3 BIN FREE R VALUE : 0.4570 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 168 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 844 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.28 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.32 REMARK 3 LOW RESOLUTION CUTOFF (A) : 3.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.35 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.631 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.85 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.825 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LSL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-02. REMARK 100 THE DEPOSITION ID IS D_1000016244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-00; 17-DEC-00 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 19-ID; 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00803, 1.00808, 1.0596; REMARK 200 1.10000 REMARK 200 MONOCHROMATOR : GRAPHITE; GRAPHITE REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15123 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M SODIUM POTASSIUM TARTRATE AND REMARK 280 0.1 M SODIUM ACETATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 33.81500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.20500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.81500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 42.20500 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 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 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 CYS A 490 -65.86 -169.58 REMARK 500 ASN A 502 17.97 -145.07 REMARK 500 ASN A 524 29.86 48.15 REMARK 500 ASP A 527 105.12 -30.99 REMARK 500 REMARK 500 REMARK: NULL DBREF 1LSL A 416 528 UNP P07996 TSP1_HUMAN 434 546 SEQRES 1 A 113 GLN ASP GLY GLY TRP SER HIS TRP SER PRO TRP SER SER SEQRES 2 A 113 CYS SER VAL THR CYS GLY ASP GLY VAL ILE THR ARG ILE SEQRES 3 A 113 ARG LEU CYS ASN SER PRO SER PRO GLN MET ASN GLY LYS SEQRES 4 A 113 PRO CYS GLU GLY GLU ALA ARG GLU THR LYS ALA CYS LYS SEQRES 5 A 113 LYS ASP ALA CYS PRO ILE ASN GLY GLY TRP GLY PRO TRP SEQRES 6 A 113 SER PRO TRP ASP ILE CYS SER VAL THR CYS GLY GLY GLY SEQRES 7 A 113 VAL GLN LYS ARG SER ARG LEU CYS ASN ASN PRO THR PRO SEQRES 8 A 113 GLN PHE GLY GLY LYS ASP CYS VAL GLY ASP VAL THR GLU SEQRES 9 A 113 ASN GLN ILE CYS ASN LYS GLN ASP CYS MODRES 1LSL THR A 432 THR GLYCOSYLATION SITE MODRES 1LSL THR A 489 THR GLYCOSYLATION SITE HET FUL A1432 10 HET FUC A1489 10 HETNAM FUL BETA-L-FUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETSYN FUL BETA-L-FUCOSE; 6-DEOXY-BETA-L-GALACTOPYRANOSE; L- HETSYN 2 FUL FUCOSE; FUCOSE; 6-DEOXY-BETA-L-GALACTOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 2 FUL C6 H12 O5 FORMUL 3 FUC C6 H12 O5 FORMUL 4 HOH *154(H2 O) SHEET 1 A 2 ASP A 435 ILE A 441 0 SHEET 2 A 2 ARG A 461 LYS A 467 -1 O LYS A 464 N ILE A 438 SHEET 1 B 2 GLY A 493 SER A 498 0 SHEET 2 B 2 THR A 518 CYS A 523 -1 O GLU A 519 N ARG A 497 SSBOND 1 CYS A 429 CYS A 466 1555 1555 2.04 SSBOND 2 CYS A 433 CYS A 471 1555 1555 2.04 SSBOND 3 CYS A 444 CYS A 456 1555 1555 2.04 SSBOND 4 CYS A 486 CYS A 523 1555 1555 2.03 SSBOND 5 CYS A 490 CYS A 528 1555 1555 2.04 SSBOND 6 CYS A 501 CYS A 513 1555 1555 2.05 LINK OG1 THR A 432 C1 FUL A1432 1555 1555 1.40 LINK OG1 THR A 489 C1 FUC A1489 1555 1555 1.41 CISPEP 1 SER A 446 PRO A 447 0 -0.07 CISPEP 2 ASN A 503 PRO A 504 0 0.29 CRYST1 67.630 84.410 37.170 90.00 108.67 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 0.014786 0.000000 0.004996 0.00000 SCALE2 0.000000 0.011847 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028398 0.00000