PDB Short entry for 1Z78 HEADER CELL ADHESION 24-MAR-05 1Z78 TITLE CRYSTAL STRUCTURE OF THE THROMBOSPONDIN-1 N-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBOSPONDIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; 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, TSP, TSP1; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FRUIT FLY; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: DROSOPHILA S2 CELLS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PMT/BIP/V5-HISA KEYWDS TSP-1, NTSP-1, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,J.WANG,J.LAWLER REVDAT 3 03-APR-24 1Z78 1 REMARK REVDAT 2 24-FEB-09 1Z78 1 VERSN REVDAT 1 17-JAN-06 1Z78 0 JRNL AUTH K.TAN,M.DUQUETTE,J.H.LIU,R.ZHANG,A.JOACHIMIAK,J.H.WANG, JRNL AUTH 2 J.LAWLER JRNL TITL THE STRUCTURES OF THE THROMBOSPONDIN-1 N-TERMINAL DOMAIN AND JRNL TITL 2 ITS COMPLEX WITH A SYNTHETIC PENTAMERIC HEPARIN. JRNL REF STRUCTURE V. 14 33 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 16407063 JRNL DOI 10.1016/J.STR.2005.09.017 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.2 REMARK 3 NUMBER OF REFLECTIONS : 14668 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) : 0.236 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1472 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2714 REMARK 3 BIN FREE R VALUE : 0.2834 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 26 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 : 1594 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 98 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.91 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) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.28 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) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.630 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.92 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.390 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1Z78 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032385. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07218 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : 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 : 17415 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.42700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.750 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: NTSP-1 STRUCTURE FROM NTSP-1/ARIXTRA COMPLEX TO BE REMARK 200 DEPOSITED REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG1500 AND 0.1 M NAAC, PH 4.6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 20.94950 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 ASN A 1 REMARK 465 ARG A 2 REMARK 465 ILE A 3 REMARK 465 PRO A 4 REMARK 465 GLU A 5 REMARK 465 SER A 6 REMARK 465 GLY A 7 REMARK 465 GLY A 8 REMARK 465 ASP A 9 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 ALA A 21 20.35 -71.41 REMARK 500 SER A 26 92.19 -172.20 REMARK 500 GLN A 117 102.51 27.28 REMARK 500 GLU A 144 -121.89 57.80 REMARK 500 ASP A 152 -127.28 69.74 REMARK 500 GLU A 154 -133.36 -133.70 REMARK 500 LYS A 155 108.25 10.86 REMARK 500 ASP A 172 54.94 -116.59 REMARK 500 VAL A 186 -116.21 -97.45 REMARK 500 REMARK 500 REMARK: NULL DBREF 1Z78 A 1 215 UNP P07996 TSP1_HUMAN 19 233 SEQRES 1 A 215 ASN ARG ILE PRO GLU SER GLY GLY ASP ASN SER VAL PHE SEQRES 2 A 215 ASP ILE PHE GLU LEU THR GLY ALA ALA ARG LYS GLY SER SEQRES 3 A 215 GLY ARG ARG LEU VAL LYS GLY PRO ASP PRO SER SER PRO SEQRES 4 A 215 ALA PHE ARG ILE GLU ASP ALA ASN LEU ILE PRO PRO VAL SEQRES 5 A 215 PRO ASP ASP LYS PHE GLN ASP LEU VAL ASP ALA VAL ARG SEQRES 6 A 215 THR GLU LYS GLY PHE LEU LEU LEU ALA SER LEU ARG GLN SEQRES 7 A 215 MET LYS LYS THR ARG GLY THR LEU LEU ALA LEU GLU ARG SEQRES 8 A 215 LYS ASP HIS SER GLY GLN VAL PHE SER VAL VAL SER ASN SEQRES 9 A 215 GLY LYS ALA GLY THR LEU ASP LEU SER LEU THR VAL GLN SEQRES 10 A 215 GLY LYS GLN HIS VAL VAL SER VAL GLU GLU ALA LEU LEU SEQRES 11 A 215 ALA THR GLY GLN TRP LYS SER ILE THR LEU PHE VAL GLN SEQRES 12 A 215 GLU ASP ARG ALA GLN LEU TYR ILE ASP CYS GLU LYS MET SEQRES 13 A 215 GLU ASN ALA GLU LEU ASP VAL PRO ILE GLN SER VAL PHE SEQRES 14 A 215 THR ARG ASP LEU ALA SER ILE ALA ARG LEU ARG ILE ALA SEQRES 15 A 215 LYS GLY GLY VAL ASN ASP ASN PHE GLN GLY VAL LEU GLN SEQRES 16 A 215 ASN VAL ARG PHE VAL PHE GLY THR THR PRO GLU ASP ILE SEQRES 17 A 215 LEU ARG ASN LYS GLY CYS SER FORMUL 2 HOH *98(H2 O) HELIX 1 1 ILE A 15 GLY A 20 1 6 HELIX 2 2 ASP A 45 ILE A 49 5 5 HELIX 3 3 PRO A 53 LYS A 68 1 16 HELIX 4 4 PRO A 164 VAL A 168 5 5 HELIX 5 5 THR A 204 ARG A 210 1 7 HELIX 6 6 ASN A 211 GLY A 213 5 3 SHEET 1 A 4 VAL A 12 ASP A 14 0 SHEET 2 A 4 GLY A 192 VAL A 200 -1 O PHE A 199 N PHE A 13 SHEET 3 A 4 ALA A 40 ILE A 43 -1 N PHE A 41 O LEU A 194 SHEET 4 A 4 ARG A 28 VAL A 31 -1 N ARG A 29 O ARG A 42 SHEET 1 B 6 VAL A 12 ASP A 14 0 SHEET 2 B 6 GLY A 192 VAL A 200 -1 O PHE A 199 N PHE A 13 SHEET 3 B 6 GLY A 69 GLN A 78 -1 N LEU A 71 O VAL A 200 SHEET 4 B 6 LYS A 136 GLN A 143 -1 O LEU A 140 N LEU A 72 SHEET 5 B 6 ARG A 146 ILE A 151 -1 O GLN A 148 N PHE A 141 SHEET 6 B 6 MET A 156 GLU A 160 -1 O ALA A 159 N ALA A 147 SHEET 1 C 5 LYS A 119 VAL A 125 0 SHEET 2 C 5 THR A 109 VAL A 116 -1 N LEU A 114 O HIS A 121 SHEET 3 C 5 GLN A 97 ASN A 104 -1 N VAL A 102 O ASP A 111 SHEET 4 C 5 ARG A 83 ARG A 91 -1 N LEU A 89 O PHE A 99 SHEET 5 C 5 ALA A 177 ILE A 181 -1 O ARG A 180 N ALA A 88 SSBOND 1 CYS A 153 CYS A 214 1555 1555 2.03 CRYST1 42.812 41.899 53.458 90.00 100.65 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 0.023358 0.000000 0.004392 0.00000 SCALE2 0.000000 0.023867 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019034 0.00000