HEADER CELL ADHESION 30-OCT-02 1N3Y TITLE CRYSTAL STRUCTURE OF THE ALPHA-X BETA2 INTEGRIN I DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRIN ALPHA-X; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: I DOMAIN; COMPND 5 SYNONYM: LEUKOCYTE ADHESION GLYCOPROTEIN P150,95 ALPHA CHAIN; COMPND 6 LEUKOCYTE ADHESION RECEPTOR P150,95; CD11C; LEU M5; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ITGAX OR CD11C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ALPHA/BETA ROSSMANN FOLD, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR T.VORUP-JENSEN,C.OSTERMEIER,M.SHIMAOKA,U.HOMMEL,T.A.SPRINGER REVDAT 4 27-OCT-21 1N3Y 1 SEQADV REVDAT 3 24-FEB-09 1N3Y 1 VERSN REVDAT 2 15-FEB-05 1N3Y 1 JRNL REVDAT 1 18-FEB-03 1N3Y 0 JRNL AUTH T.VORUP-JENSEN,C.OSTERMEIER,M.SHIMAOKA,U.HOMMEL,T.A.SPRINGER JRNL TITL STRUCTURE AND ALLOSTERIC REGULATION OF THE ALPHA X BETA 2 JRNL TITL 2 INTEGRIN I DOMAIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 1873 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 12554829 JRNL DOI 10.1073/PNAS.0237387100 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.72 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 : 32311 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1601 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 32357 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5055 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 283 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1512 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 291 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.05000 REMARK 3 B22 (A**2) : -2.05000 REMARK 3 B33 (A**2) : 4.10000 REMARK 3 B12 (A**2) : -0.74000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.240 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.980 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.230 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.450 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 61.54 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1N3Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-NOV-02. REMARK 100 THE DEPOSITION ID IS D_1000017488. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : OSMIC MIRRORS 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 : 32357 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22900 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: CNS REMARK 200 STARTING MODEL: IN-HOUSE STRUCTURE OF A MAC1 I DOMAIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, GLYCEROL, SODIUM REMARK 280 ACETATE, EDTA, PH 5.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 21.92533 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 43.85067 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.88800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 54.81333 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 10.96267 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 GLY A 122 REMARK 465 SER A 123 REMARK 465 HIS A 124 REMARK 465 MET A 125 REMARK 465 ALA A 126 REMARK 465 SER A 127 REMARK 465 ARG A 128 REMARK 465 GLU A 318 REMARK 465 GLY A 319 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 175 -114.51 -150.92 REMARK 500 ASN A 192 75.68 -151.86 REMARK 500 SER A 199 49.00 -108.49 REMARK 500 GLN A 204 174.32 73.05 REMARK 500 ARG A 219 -57.62 -144.80 REMARK 500 ASN A 275 -145.74 -87.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 1N3Y A 128 319 UNP P20702 ITAX_HUMAN 147 338 SEQADV 1N3Y GLY A 122 UNP P20702 CLONING ARTIFACT SEQADV 1N3Y SER A 123 UNP P20702 CLONING ARTIFACT SEQADV 1N3Y HIS A 124 UNP P20702 CLONING ARTIFACT SEQADV 1N3Y MET A 125 UNP P20702 CLONING ARTIFACT SEQADV 1N3Y ALA A 126 UNP P20702 CLONING ARTIFACT SEQADV 1N3Y SER A 127 UNP P20702 CLONING ARTIFACT SEQADV 1N3Y SER A 190 UNP P20702 THR 209 ENGINEERED MUTATION SEQADV 1N3Y ALA A 232 UNP P20702 THR 251 ENGINEERED MUTATION SEQRES 1 A 198 GLY SER HIS MET ALA SER ARG GLN GLU GLN ASP ILE VAL SEQRES 2 A 198 PHE LEU ILE ASP GLY SER GLY SER ILE SER SER ARG ASN SEQRES 3 A 198 PHE ALA THR MET MET ASN PHE VAL ARG ALA VAL ILE SER SEQRES 4 A 198 GLN PHE GLN ARG PRO SER THR GLN PHE SER LEU MET GLN SEQRES 5 A 198 PHE SER ASN LYS PHE GLN THR HIS PHE THR PHE GLU GLU SEQRES 6 A 198 PHE ARG ARG SER SER ASN PRO LEU SER LEU LEU ALA SER SEQRES 7 A 198 VAL HIS GLN LEU GLN GLY PHE THR TYR THR ALA THR ALA SEQRES 8 A 198 ILE GLN ASN VAL VAL HIS ARG LEU PHE HIS ALA SER TYR SEQRES 9 A 198 GLY ALA ARG ARG ASP ALA ALA LYS ILE LEU ILE VAL ILE SEQRES 10 A 198 THR ASP GLY LYS LYS GLU GLY ASP SER LEU ASP TYR LYS SEQRES 11 A 198 ASP VAL ILE PRO MET ALA ASP ALA ALA GLY ILE ILE ARG SEQRES 12 A 198 TYR ALA ILE GLY VAL GLY LEU ALA PHE GLN ASN ARG ASN SEQRES 13 A 198 SER TRP LYS GLU LEU ASN ASP ILE ALA SER LYS PRO SER SEQRES 14 A 198 GLN GLU HIS ILE PHE LYS VAL GLU ASP PHE ASP ALA LEU SEQRES 15 A 198 LYS ASP ILE GLN ASN GLN LEU LYS GLU LYS ILE PHE ALA SEQRES 16 A 198 ILE GLU GLY FORMUL 2 HOH *291(H2 O) HELIX 1 1 SER A 144 SER A 160 1 17 HELIX 2 2 THR A 183 SER A 190 1 8 HELIX 3 3 ASN A 192 ALA A 198 5 7 HELIX 4 4 TYR A 208 HIS A 218 1 11 HELIX 5 5 HIS A 222 GLY A 226 5 5 HELIX 6 6 ASP A 249 ALA A 260 1 12 HELIX 7 7 LEU A 271 ASN A 275 5 5 HELIX 8 8 SER A 278 ALA A 286 1 9 HELIX 9 9 SER A 290 GLU A 292 5 3 HELIX 10 10 ASP A 299 ASP A 305 5 7 HELIX 11 11 ILE A 306 ALA A 316 1 11 SHEET 1 A 6 PHE A 178 PHE A 182 0 SHEET 2 A 6 THR A 167 PHE A 174 -1 N GLN A 173 O GLN A 179 SHEET 3 A 6 GLN A 131 ASP A 138 1 N ILE A 133 O GLN A 168 SHEET 4 A 6 ALA A 232 THR A 239 1 O ILE A 236 N LEU A 136 SHEET 5 A 6 ILE A 263 VAL A 269 1 O ILE A 263 N LEU A 235 SHEET 6 A 6 ILE A 294 VAL A 297 1 O PHE A 295 N GLY A 268 CISPEP 1 ARG A 164 PRO A 165 0 -0.17 CISPEP 2 LYS A 288 PRO A 289 0 0.11 CRYST1 84.694 84.694 65.776 90.00 90.00 120.00 P 61 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 0.011807 0.006817 0.000000 0.00000 SCALE2 0.000000 0.013634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015203 0.00000 MASTER 268 0 0 11 6 0 0 6 0 0 0 16 END