PDB Short entry for 1M1U HEADER CELL ADHESION 20-JUN-02 1M1U TITLE AN ISOLEUCINE-BASED ALLOSTERIC SWITCH CONTROLS AFFINITY AND SHAPE TITLE 2 SHIFTING IN INTEGRIN CD11B A-DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRIN ALPHA-M; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CD11B A-DOMAIN, RESIDUES 123-315; COMPND 5 SYNONYM: CD11B; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5A; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX4T-1 KEYWDS INTEGRIN, CELL ADHESION PROTEIN, GLYCOPROTEIN, A-DOMAIN, CD11B, CELL KEYWDS 2 ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR J.-P.XIONG,R.LI,M.ESSAFI,T.STEHLE,M.A.ARNAOUT REVDAT 5 14-FEB-24 1M1U 1 REMARK REVDAT 4 27-OCT-21 1M1U 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1M1U 1 VERSN REVDAT 2 01-APR-03 1M1U 1 JRNL REVDAT 1 07-AUG-02 1M1U 0 JRNL AUTH J.P.XIONG,R.LI,M.ESSAFI,T.STEHLE,M.A.ARNAOUT JRNL TITL AN ISOLEUCINE-BASED ALLOSTERIC SWITCH CONTROLS AFFINITY AND JRNL TITL 2 SHAPE SHIFTING IN INTEGRIN CD11B A-DOMAIN. JRNL REF J.BIOL.CHEM. V. 275 38762 2000 JRNL REFN ISSN 0021-9258 JRNL PMID 11034990 JRNL DOI 10.1074/JBC.C000563200 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 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 : 7759 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGTHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 315 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 : 1490 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 39 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 1M1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016493. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7963 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1IDO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG8K, 0.1M TRIS-HCL 8.2, 5MM REMARK 280 CACL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, PH 8.2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 47.40000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 71.10000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.70000 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 121 REMARK 465 SER A 122 REMARK 465 GLU A 123 REMARK 465 ALA A 124 REMARK 465 LEU A 125 REMARK 465 ARG A 126 REMARK 465 GLY A 127 REMARK 465 SER A 128 REMARK 465 PRO A 129 REMARK 465 GLN A 130 REMARK 465 GLU A 131 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 LYS A 165 96.19 -66.87 REMARK 500 SER A 177 -110.20 -154.03 REMARK 500 ASN A 192 77.92 -150.58 REMARK 500 PRO A 193 44.24 -73.65 REMARK 500 LEU A 206 178.57 68.38 REMARK 500 PHE A 223 34.74 -82.54 REMARK 500 ASN A 232 -22.10 84.12 REMARK 500 PHE A 302 -0.85 -59.13 REMARK 500 REMARK 500 REMARK: NULL 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 400 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 142 OG REMARK 620 2 SER A 144 OG 97.1 REMARK 620 3 THR A 209 OG1 85.6 172.5 REMARK 620 4 GLU A 314 OE2 83.4 94.7 78.6 REMARK 620 5 HOH A 431 O 165.2 89.4 86.5 82.9 REMARK 620 6 HOH A 449 O 101.7 96.5 89.8 167.0 90.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IDO RELATED DB: PDB REMARK 900 C-TERMINAL IFA SEQUENCE TRUNCATION REMARK 900 RELATED ID: 1M1X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EXTRACELLULAR SEGMENT OF INTEGRIN ALPHA REMARK 900 VBETA3 IN COMPLEX WITH AN ARG-GLY-ASP LIGAND DBREF 1M1U A 123 315 UNP P11215 ITAM_HUMAN 139 331 SEQADV 1M1U GLY A 121 UNP P11215 CLONING ARTIFACT SEQADV 1M1U SER A 122 UNP P11215 CLONING ARTIFACT SEQADV 1M1U SER A 128 UNP P11215 CYS 144 ENGINEERED MUTATION SEQRES 1 A 195 GLY SER GLU ALA LEU ARG GLY SER PRO GLN GLU ASP SER SEQRES 2 A 195 ASP ILE ALA PHE LEU ILE ASP GLY SER GLY SER ILE ILE SEQRES 3 A 195 PRO HIS ASP PHE ARG ARG MET LYS GLU PHE VAL SER THR SEQRES 4 A 195 VAL MET GLU GLN LEU LYS LYS SER LYS THR LEU PHE SER SEQRES 5 A 195 LEU MET GLN TYR SER GLU GLU PHE ARG ILE HIS PHE THR SEQRES 6 A 195 PHE LYS GLU PHE GLN ASN ASN PRO ASN PRO ARG SER LEU SEQRES 7 A 195 VAL LYS PRO ILE THR GLN LEU LEU GLY ARG THR HIS THR SEQRES 8 A 195 ALA THR GLY ILE ARG LYS VAL VAL ARG GLU LEU PHE ASN SEQRES 9 A 195 ILE THR ASN GLY ALA ARG LYS ASN ALA PHE LYS ILE LEU SEQRES 10 A 195 VAL VAL ILE THR ASP GLY GLU LYS PHE GLY ASP PRO LEU SEQRES 11 A 195 GLY TYR GLU ASP VAL ILE PRO GLU ALA ASP ARG GLU GLY SEQRES 12 A 195 VAL ILE ARG TYR VAL ILE GLY VAL GLY ASP ALA PHE ARG SEQRES 13 A 195 SER GLU LYS SER ARG GLN GLU LEU ASN THR ILE ALA SER SEQRES 14 A 195 LYS PRO PRO ARG ASP HIS VAL PHE GLN VAL ASN ASN PHE SEQRES 15 A 195 GLU ALA LEU LYS THR ILE GLN ASN GLN LEU ARG GLU LYS HET CA A 400 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *39(H2 O) HELIX 1 1 ILE A 146 LEU A 164 1 19 HELIX 2 2 THR A 185 ASN A 192 1 8 HELIX 3 3 ASN A 194 LYS A 200 1 7 HELIX 4 4 HIS A 210 LEU A 222 1 13 HELIX 5 5 ASN A 224 GLY A 228 5 5 HELIX 6 6 GLY A 251 ASP A 254 5 4 HELIX 7 7 VAL A 255 GLU A 262 1 8 HELIX 8 8 SER A 277 ALA A 288 1 12 HELIX 9 9 PRO A 291 ASP A 294 5 4 HELIX 10 10 GLU A 303 LEU A 312 1 10 HELIX 11 11 ARG A 313 LYS A 315 5 3 SHEET 1 A 6 PHE A 180 PHE A 184 0 SHEET 2 A 6 THR A 169 TYR A 176 -1 N GLN A 175 O ARG A 181 SHEET 3 A 6 SER A 133 ASP A 140 1 N ILE A 135 O LEU A 170 SHEET 4 A 6 PHE A 234 THR A 241 1 O VAL A 238 N LEU A 138 SHEET 5 A 6 VAL A 264 GLY A 270 1 O ILE A 265 N LEU A 237 SHEET 6 A 6 VAL A 296 GLN A 298 1 O PHE A 297 N GLY A 270 LINK OG SER A 142 CA CA A 400 1555 1555 2.31 LINK OG SER A 144 CA CA A 400 1555 1555 2.30 LINK OG1 THR A 209 CA CA A 400 1555 1555 2.35 LINK OE2 GLU A 314 CA CA A 400 4455 1555 2.23 LINK CA CA A 400 O HOH A 431 1555 1555 2.21 LINK CA CA A 400 O HOH A 449 1555 1555 2.26 CISPEP 1 LYS A 290 PRO A 291 0 -1.03 SITE 1 AC1 6 SER A 142 SER A 144 THR A 209 GLU A 314 SITE 2 AC1 6 HOH A 431 HOH A 449 CRYST1 45.700 45.700 94.800 90.00 90.00 90.00 P 43 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 0.021882 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010549 0.00000