HEADER IMMUNE SYSTEM 15-SEP-02 1MQA TITLE CRYSTAL STRUCTURE OF HIGH AFFINITY ALPHAL I DOMAIN IN THE ABSENCE OF TITLE 2 LIGAND OR METAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRIN ALPHA-L; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: INTEGRIN ALPHAL I DOMAIN; COMPND 5 SYNONYM: LEUKOCYTE ADHESION GLYCOPROTEIN LFA-1 ALPHA CHAIN; LEUKOCYTE COMPND 6 FUNCTION ASSOCIATED MOLECULE 1, ALPHA CHAIN; CD11A; 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: LFA-1 (ALPHALBETA2); 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: PET11 KEYWDS DESIGNED DISULFIDE BRIDGE, ROSSMANN FOLD, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.SHIMAOKA,T.XIAO,J.-H.LIU,Y.YANG,Y.DONG,C.-D.JUN,R.ZHANG,J.TAKAGI, AUTHOR 2 J.-H.WANG,T.A.SPRINGER REVDAT 4 06-NOV-24 1MQA 1 REMARK REVDAT 3 27-OCT-21 1MQA 1 SEQADV REVDAT 2 24-FEB-09 1MQA 1 VERSN REVDAT 1 14-JAN-03 1MQA 0 JRNL AUTH M.SHIMAOKA,T.XIAO,J.-H.LIU,Y.YANG,Y.DONG,C.-D.JUN, JRNL AUTH 2 A.MCCORMACK,R.ZHANG,A.JOACHIMIAK,J.TAKAGI,J.-H.WANG, JRNL AUTH 3 T.A.SPRINGER JRNL TITL STRUCTURES OF THE AL I DOMAIN AND ITS COMPLEX WITH ICAM-1 JRNL TITL 2 REVEAL A SHAPE-SHIFTING PATHWAY FOR INTEGRIN REGULATION JRNL REF CELL(CAMBRIDGE,MASS.) V. 112 99 2003 JRNL REFN ISSN 0092-8674 JRNL PMID 12526797 JRNL DOI 10.1016/S0092-8674(02)01257-6 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.36 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) (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 6678 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 SET) : 0.249 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.900 REMARK 3 FREE R VALUE TEST SET COUNT : 727 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 732 REMARK 3 BIN R VALUE (WORKING SET) : 0.4000 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 97 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1388 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 20.75000 REMARK 3 B22 (A**2) : -7.73000 REMARK 3 B33 (A**2) : -13.02000 REMARK 3 B12 (A**2) : 0.00000 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) : 0.39 REMARK 3 ESD FROM SIGMAA (A) : 0.55 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) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.51 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.070 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : GROUP 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 : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 29.55 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.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MAXIMUM LIKELIHOOD REFINEMENT TARGET REMARK 4 REMARK 4 1MQA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1000017095. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 0.9700 REMARK 200 MONOCHROMATOR : NI MIRROR + NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7271 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.18400 REMARK 200 R SYM (I) : 0.18400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.41300 REMARK 200 R SYM FOR SHELL (I) : 0.41300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: 1MQ9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M AMMONIUM PHOSPHATE, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP AT 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 27.02950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.02950 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.93200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.66200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.93200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.66200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.02950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.93200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 60.66200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 27.02950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.93200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 60.66200 REMARK 290 SMTRY3 8 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 GLU A 301 REMARK 465 LEU A 302 REMARK 465 GLN A 303 REMARK 465 LYS A 304 REMARK 465 LYS A 305 REMARK 465 ILE A 306 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 174 -121.11 -172.42 REMARK 500 PHE A 181 141.58 -172.56 REMARK 500 LYS A 190 18.62 59.30 REMARK 500 LEU A 204 -152.66 -122.34 REMARK 500 LEU A 205 -175.92 -61.99 REMARK 500 ILE A 248 43.28 -104.70 REMARK 500 THR A 267 133.21 173.05 REMARK 500 PHE A 292 56.14 35.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MQ8 RELATED DB: PDB REMARK 900 RELATED ID: 1MQ9 RELATED DB: PDB DBREF 1MQA A 128 306 UNP P20701 ITAL_HUMAN 153 331 SEQADV 1MQA MET A 127 UNP P20701 CLONING ARTIFACT SEQADV 1MQA CYS A 287 UNP P20701 LYS 312 ENGINEERED MUTATION SEQADV 1MQA CYS A 294 UNP P20701 LYS 319 ENGINEERED MUTATION SEQRES 1 A 180 MET GLY ASN VAL ASP LEU VAL PHE LEU PHE ASP GLY SER SEQRES 2 A 180 MET SER LEU GLN PRO ASP GLU PHE GLN LYS ILE LEU ASP SEQRES 3 A 180 PHE MET LYS ASP VAL MET LYS LYS LEU SER ASN THR SER SEQRES 4 A 180 TYR GLN PHE ALA ALA VAL GLN PHE SER THR SER TYR LYS SEQRES 5 A 180 THR GLU PHE ASP PHE SER ASP TYR VAL LYS ARG LYS ASP SEQRES 6 A 180 PRO ASP ALA LEU LEU LYS HIS VAL LYS HIS MET LEU LEU SEQRES 7 A 180 LEU THR ASN THR PHE GLY ALA ILE ASN TYR VAL ALA THR SEQRES 8 A 180 GLU VAL PHE ARG GLU GLU LEU GLY ALA ARG PRO ASP ALA SEQRES 9 A 180 THR LYS VAL LEU ILE ILE ILE THR ASP GLY GLU ALA THR SEQRES 10 A 180 ASP SER GLY ASN ILE ASP ALA ALA LYS ASP ILE ILE ARG SEQRES 11 A 180 TYR ILE ILE GLY ILE GLY LYS HIS PHE GLN THR LYS GLU SEQRES 12 A 180 SER GLN GLU THR LEU HIS LYS PHE ALA SER LYS PRO ALA SEQRES 13 A 180 SER GLU PHE VAL CYS ILE LEU ASP THR PHE GLU CYS LEU SEQRES 14 A 180 LYS ASP LEU PHE THR GLU LEU GLN LYS LYS ILE FORMUL 2 HOH *31(H2 O) HELIX 1 1 GLN A 143 LEU A 161 1 19 HELIX 2 2 ASP A 182 LYS A 190 1 9 HELIX 3 3 ASP A 191 LEU A 196 1 6 HELIX 4 4 ASN A 207 VAL A 219 1 13 HELIX 5 5 ARG A 221 GLY A 225 5 5 HELIX 6 6 ILE A 248 LYS A 252 5 5 HELIX 7 7 SER A 270 HIS A 275 5 6 HELIX 8 8 PRO A 281 PHE A 285 1 5 SHEET 1 A 6 TYR A 177 PHE A 181 0 SHEET 2 A 6 TYR A 166 PHE A 173 -1 N ALA A 170 O PHE A 181 SHEET 3 A 6 VAL A 130 ASP A 137 1 N PHE A 134 O VAL A 171 SHEET 4 A 6 THR A 231 THR A 238 1 O VAL A 233 N ASP A 131 SHEET 5 A 6 ILE A 255 GLY A 260 1 O TYR A 257 N ILE A 236 SHEET 6 A 6 VAL A 286 ILE A 288 1 O CYS A 287 N ILE A 258 SSBOND 1 CYS A 287 CYS A 294 1555 1555 2.04 CISPEP 1 LYS A 280 PRO A 281 0 -0.78 CRYST1 61.864 121.324 54.059 90.00 90.00 90.00 C 2 2 21 8 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 0.016164 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008242 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018498 0.00000