HEADER CELL ADHESION 25-APR-01 1IJ9 TITLE HIGHLY HYDRATED HUMAN VCAM-1 FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR CELL ADHESION PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VCAM-D1,D2 (INTEGRIN BINDING FRAGMENT); COMPND 5 SYNONYM: VCAM-1; COMPND 6 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INTEGRIN SOLVATION, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR P.TAYLOR,M.BILSLAND,M.D.WALKINSHAW REVDAT 5 16-AUG-23 1IJ9 1 REMARK REVDAT 4 24-FEB-09 1IJ9 1 VERSN REVDAT 3 01-APR-03 1IJ9 1 JRNL REVDAT 2 07-NOV-01 1IJ9 1 REVDAT 1 02-MAY-01 1IJ9 0 JRNL AUTH P.TAYLOR,M.BILSLAND,M.D.WALKINSHAW JRNL TITL A NEW CONFORMATION OF THE INTEGRIN-BINDING FRAGMENT OF HUMAN JRNL TITL 2 VCAM-1 CRYSTALLIZES IN A HIGHLY HYDRATED PACKING JRNL TITL 3 ARRANGEMENT. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 1579 2001 JRNL REFN ISSN 0907-4449 JRNL PMID 11679722 JRNL DOI 10.1107/S0907444901011209 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12530 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1293 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1533 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 63.00 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.311 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.71 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.058 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 1IJ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013325. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 183518 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 24.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.440 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.26 REMARK 200 R MERGE FOR SHELL (I) : 0.59600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.140 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: 1VCA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 82.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 7.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, TRIS, AMMONIUM SULPHATE, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.32533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.65067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.65067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 15.32533 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 SER A 9 -8.14 -146.93 REMARK 500 ASP A 40 82.17 63.42 REMARK 500 GLU A 76 -97.98 66.22 REMARK 500 PHE A 91 58.71 -154.38 REMARK 500 ASP A 117 70.64 47.42 REMARK 500 LEU A 141 135.02 -34.75 REMARK 500 GLU A 142 88.05 -46.18 REMARK 500 ASP A 143 93.32 173.51 REMARK 500 ALA A 144 -106.20 -81.32 REMARK 500 ASP A 145 -43.30 168.79 REMARK 500 GLU A 179 140.04 -24.08 REMARK 500 MET A 180 61.73 -101.16 REMARK 500 ASP A 181 -89.97 59.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 1IJ9 A 1 196 UNP P19320 VCAM1_HUMAN 25 220 SEQRES 1 A 196 PHE LYS ILE GLU THR THR PRO GLU SER ARG TYR LEU ALA SEQRES 2 A 196 GLN ILE GLY ASP SER VAL SER LEU THR CYS SER THR THR SEQRES 3 A 196 GLY CYS GLU SER PRO PHE PHE SER TRP ARG THR GLN ILE SEQRES 4 A 196 ASP SER PRO LEU ASN GLY LYS VAL THR ASN GLU GLY THR SEQRES 5 A 196 THR SER THR LEU THR MET ASN PRO VAL SER PHE GLY ASN SEQRES 6 A 196 GLU HIS SER TYR LEU CYS THR ALA THR CYS GLU SER ARG SEQRES 7 A 196 LYS LEU GLU LYS GLY ILE GLN VAL GLU ILE TYR SER PHE SEQRES 8 A 196 PRO LYS ASP PRO GLU ILE HIS LEU SER GLY PRO LEU GLU SEQRES 9 A 196 ALA GLY LYS PRO ILE THR VAL LYS CYS SER VAL ALA ASP SEQRES 10 A 196 VAL TYR PRO PHE ASP ARG LEU GLU ILE ASP LEU LEU LYS SEQRES 11 A 196 GLY ASP HIS LEU MET LYS SER GLN GLU PHE LEU GLU ASP SEQRES 12 A 196 ALA ASP ARG LYS SER LEU GLU THR LYS SER LEU GLU VAL SEQRES 13 A 196 THR PHE THR PRO VAL ILE GLU ASP ILE GLY LYS VAL LEU SEQRES 14 A 196 VAL CYS ARG ALA LYS LEU HIS ILE ASP GLU MET ASP SER SEQRES 15 A 196 VAL PRO THR VAL ARG GLN ALA VAL LYS GLU LEU GLN VAL SEQRES 16 A 196 TYR FORMUL 2 HOH *50(H2 O) HELIX 1 1 SER A 62 GLU A 66 5 5 HELIX 2 2 PRO A 120 ASP A 122 5 3 HELIX 3 3 VAL A 161 ILE A 165 5 5 SHEET 1 A 4 LYS A 2 THR A 6 0 SHEET 2 A 4 VAL A 19 THR A 26 -1 N THR A 22 O THR A 6 SHEET 3 A 4 THR A 53 MET A 58 -1 N SER A 54 O CYS A 23 SHEET 4 A 4 LYS A 46 GLU A 50 -1 O LYS A 46 N THR A 57 SHEET 1 B 4 ARG A 10 GLN A 14 0 SHEET 2 B 4 ARG A 78 TYR A 89 1 O GLN A 85 N TYR A 11 SHEET 3 B 4 SER A 68 CYS A 75 -1 N TYR A 69 O ILE A 84 SHEET 4 B 4 PHE A 32 THR A 37 -1 N PHE A 32 O THR A 74 SHEET 1 C 3 GLU A 96 LEU A 99 0 SHEET 2 C 3 ILE A 109 VAL A 118 -1 O LYS A 112 N HIS A 98 SHEET 3 C 3 GLU A 150 PHE A 158 -1 O GLU A 150 N VAL A 118 SHEET 1 D 4 HIS A 133 GLU A 139 0 SHEET 2 D 4 LEU A 124 LYS A 130 -1 O ILE A 126 N GLN A 138 SHEET 3 D 4 VAL A 168 LEU A 175 -1 N VAL A 170 O LEU A 129 SHEET 4 D 4 VAL A 186 GLU A 192 -1 O ARG A 187 N ALA A 173 SSBOND 1 CYS A 23 CYS A 71 1555 1555 2.03 SSBOND 2 CYS A 28 CYS A 75 1555 1555 2.03 SSBOND 3 CYS A 113 CYS A 171 1555 1555 2.02 CISPEP 1 THR A 6 PRO A 7 0 0.18 CISPEP 2 ASN A 59 PRO A 60 0 0.02 CISPEP 3 TYR A 119 PRO A 120 0 -0.11 CRYST1 152.939 152.939 45.976 90.00 90.00 120.00 P 31 2 1 6 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 0.006539 0.003775 0.000000 0.00000 SCALE2 0.000000 0.007550 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021750 0.00000