HEADER CELL ADHESION PROTEIN 09-APR-96 1JLM TITLE I-DOMAIN FROM INTEGRIN CR3, MN2+ BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: I-DOMAIN; COMPND 5 SYNONYM: INTEGRIN ALPHA-M; 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; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS INTEGRIN, CELL ADHESION PROTEIN, GLYCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.-O.LEE,R.LIDDINGTON REVDAT 4 09-AUG-23 1JLM 1 REMARK LINK REVDAT 3 21-MAR-18 1JLM 1 REMARK REVDAT 2 24-FEB-09 1JLM 1 VERSN REVDAT 1 11-JAN-97 1JLM 0 JRNL AUTH J.O.LEE,L.A.BANKSTON,M.A.ARNAOUT,R.C.LIDDINGTON JRNL TITL TWO CONFORMATIONS OF THE INTEGRIN A-DOMAIN (I-DOMAIN): A JRNL TITL 2 PATHWAY FOR ACTIVATION? JRNL REF STRUCTURE V. 3 1333 1995 JRNL REFN ISSN 0969-2126 JRNL PMID 8747460 JRNL DOI 10.1016/S0969-2126(01)00271-4 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.O.LEE,P.RIEU,M.A.ARNAOUT,R.LIDDINGTON REMARK 1 TITL CRYSTAL STRUCTURE OF THE A DOMAIN FROM THE ALPHA SUBUNIT OF REMARK 1 TITL 2 INTEGRIN CR3 (CD11B/CD18) REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 80 631 1995 REMARK 1 REFN ISSN 0092-8674 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.MICHISHITA,V.VIDEM,M.A.ARNAOUT REMARK 1 TITL A NOVEL DIVALENT CATION-BINDING SITE IN THE A DOMAIN OF THE REMARK 1 TITL 2 BETA 2 INTEGRIN CR3 (CD11B/CD18) IS ESSENTIAL FOR LIGAND REMARK 1 TITL 3 BINDING REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 72 857 1993 REMARK 1 REFN ISSN 0092-8674 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.00 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) (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 11948 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 1515 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 105 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.00 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) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.750 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.600 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 1JLM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174342. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 REMARK 200 MONOCHROMATOR : NULL 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 : 12933 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 12.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.26900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 1IDO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 67.50000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.50000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.55000 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 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 127 REMARK 465 CYS 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 SER A 177 -99.87 -148.80 REMARK 500 ASN A 192 69.98 -155.85 REMARK 500 PRO A 193 48.98 -70.72 REMARK 500 LEU A 206 168.54 66.59 REMARK 500 ASN A 232 0.65 88.73 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 MN A 400 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 142 OG REMARK 620 2 SER A 144 OG 95.7 REMARK 620 3 ASP A 242 OD1 93.4 92.4 REMARK 620 4 HOH A 404 O 75.3 169.5 82.8 REMARK 620 5 HOH A 408 O 94.3 87.4 172.4 98.6 REMARK 620 6 HOH A 409 O 177.6 83.0 88.7 106.1 83.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: MN REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: MANGANESE BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 400 DBREF 1JLM A 127 318 UNP P11215 ITAM_HUMAN 143 334 SEQRES 1 A 192 GLY CYS PRO GLN GLU ASP SER ASP ILE ALA PHE LEU ILE SEQRES 2 A 192 ASP GLY SER GLY SER ILE ILE PRO HIS ASP PHE ARG ARG SEQRES 3 A 192 MET LYS GLU PHE VAL SER THR VAL MET GLU GLN LEU LYS SEQRES 4 A 192 LYS SER LYS THR LEU PHE SER LEU MET GLN TYR SER GLU SEQRES 5 A 192 GLU PHE ARG ILE HIS PHE THR PHE LYS GLU PHE GLN ASN SEQRES 6 A 192 ASN PRO ASN PRO ARG SER LEU VAL LYS PRO ILE THR GLN SEQRES 7 A 192 LEU LEU GLY ARG THR HIS THR ALA THR GLY ILE ARG LYS SEQRES 8 A 192 VAL VAL ARG GLU LEU PHE ASN ILE THR ASN GLY ALA ARG SEQRES 9 A 192 LYS ASN ALA PHE LYS ILE LEU VAL VAL ILE THR ASP GLY SEQRES 10 A 192 GLU LYS PHE GLY ASP PRO LEU GLY TYR GLU ASP VAL ILE SEQRES 11 A 192 PRO GLU ALA ASP ARG GLU GLY VAL ILE ARG TYR VAL ILE SEQRES 12 A 192 GLY VAL GLY ASP ALA PHE ARG SER GLU LYS SER ARG GLN SEQRES 13 A 192 GLU LEU ASN THR ILE ALA SER LYS PRO PRO ARG ASP HIS SEQRES 14 A 192 VAL PHE GLN VAL ASN ASN PHE GLU ALA LEU LYS THR ILE SEQRES 15 A 192 GLN ASN GLN LEU ARG GLU LYS ILE PHE ALA HET MN A 400 1 HETNAM MN MANGANESE (II) ION FORMUL 2 MN MN 2+ FORMUL 3 HOH *105(H2 O) HELIX 1 1 HIS A 148 GLN A 163 1 16 HELIX 2 2 PHE A 186 ASN A 192 1 7 HELIX 3 3 ARG A 196 LYS A 200 1 5 HELIX 4 4 THR A 211 LEU A 222 1 12 HELIX 5 5 TYR A 252 ARG A 261 1 10 HELIX 6 6 GLU A 278 ILE A 287 1 10 HELIX 7 7 GLU A 303 ALA A 318 1 16 SHEET 1 A 6 HIS A 295 VAL A 299 0 SHEET 2 A 6 ILE A 265 VAL A 271 1 N VAL A 268 O PHE A 297 SHEET 3 A 6 PHE A 234 THR A 241 1 N LYS A 235 O ILE A 265 SHEET 4 A 6 ASP A 132 GLY A 141 1 N ASP A 134 O PHE A 234 SHEET 5 A 6 LYS A 168 TYR A 176 1 N LEU A 170 O SER A 133 SHEET 6 A 6 PHE A 180 ILE A 182 -1 N ARG A 181 O GLN A 175 LINK OG SER A 142 MN MN A 400 1555 1555 2.29 LINK OG SER A 144 MN MN A 400 1555 1555 2.09 LINK OD1 ASP A 242 MN MN A 400 1555 1555 2.27 LINK MN MN A 400 O HOH A 404 1555 1555 2.07 LINK MN MN A 400 O HOH A 408 1555 1555 2.42 LINK MN MN A 400 O HOH A 409 1555 1555 2.14 CISPEP 1 LYS A 290 PRO A 291 0 -0.37 SITE 1 MN 7 MN A 400 SER A 142 SER A 144 ASP A 242 SITE 2 MN 7 HOH A 404 HOH A 408 HOH A 409 SITE 1 AC1 6 SER A 142 SER A 144 ASP A 242 HOH A 404 SITE 2 AC1 6 HOH A 408 HOH A 409 CRYST1 135.000 37.100 38.500 90.00 92.60 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 0.007407 0.000000 0.000336 0.00000 SCALE2 0.000000 0.026954 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026001 0.00000