HEADER CELL ADHESION 12-MAY-99 1QCY TITLE THE CRYSTAL STRUCTURE OF THE I-DOMAIN OF HUMAN INTEGRIN ALPHA1BETA1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: I-DOMAIN OF INTEGRIN ALPHA1BETA1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FRAGMENT, I-DOMAIN OF HUMAN INTEGRIN A1B1; COMPND 5 ENGINEERED: YES; COMPND 6 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_VECTOR_TYPE: PLASMID KEYWDS DINUCLEOTIDE BINDING FOLD, ROSSMANN FOLD, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR J.A.KANKARE,T.A.SALMINEN,Y.NYMALM,J.KAEPYLAE,J.HEINO,M.S.JOHNSON REVDAT 4 12-NOV-14 1QCY 1 KEYWDS REVDAT 3 24-FEB-09 1QCY 1 VERSN REVDAT 2 04-JAN-05 1QCY 1 JRNL REMARK REVDAT 1 02-SEP-03 1QCY 0 JRNL AUTH Y.NYMALM,J.S.PURANEN,T.K.M.NYHOLM,J.KAEPYLAE,H.KIDRON, JRNL AUTH 2 O.T.PENTIKAEINEN,T.T.AIRENNE,J.HEINO,J.P.SLOTTE,M.S.JOHNSON, JRNL AUTH 3 T.A.SALMINEN JRNL TITL JARARHAGIN-DERIVED RKKH PEPTIDES INDUCE STRUCTURAL CHANGES JRNL TITL 2 IN A1I DOMAIN OF HUMAN INTEGRIN A1B1 JRNL REF J.BIOL.CHEM. V. 279 7962 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 14660600 JRNL DOI 10.1074/JBC.M312912200 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.4 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 500.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 374683.350 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 9471 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) : 0.200 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.500 REMARK 3 FREE R VALUE TEST SET COUNT : 995 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.38 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 796 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 94 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1514 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.52000 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : -2.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.92000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 6.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.100 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 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) : 1.380 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.210 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.250 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.250 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 29.22 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 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QCY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-99. REMARK 100 THE RCSB ID CODE IS RCSB009087. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9471 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 500.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05800 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) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.9 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, NA-ACETATE, GLYCEROL, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298.0K 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 37.22850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.92900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.22850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.92900 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 300 REMARK: I-DOMAIN IS A FRAGMENT OF ALPHA1 SUBUNIT OF THE LARGE REMARK 300 INTEGRIN HETERODIMER 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 GLN A 178 -133.95 -114.98 REMARK 500 MET A 221 69.11 -104.39 REMARK 500 ASP A 258 41.95 -108.62 REMARK 500 THR A 307 -57.50 121.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 36 DISTANCE = 5.19 ANGSTROMS 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 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 152 OG REMARK 620 2 SER A 154 OG 88.0 REMARK 620 3 ASP A 253 OD1 71.4 78.1 REMARK 620 4 HOH A 5 O 71.1 146.3 70.4 REMARK 620 5 HOH A 47 O 160.9 95.6 90.9 96.5 REMARK 620 6 HOH A 48 O 112.2 97.9 174.7 114.3 86.0 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 MG A 101 DBREF 1QCY A 141 333 UNP P56199 ITA1_HUMAN 141 333 SEQADV 1QCY ALA A 218 UNP P56199 ARG 218 SEE REMARK 999 SEQRES 1 A 193 THR GLN LEU ASP ILE VAL ILE VAL LEU ASP GLY SER ASN SEQRES 2 A 193 SER ILE TYR PRO TRP ASP SER VAL THR ALA PHE LEU ASN SEQRES 3 A 193 ASP LEU LEU LYS ARG MET ASP ILE GLY PRO LYS GLN THR SEQRES 4 A 193 GLN VAL GLY ILE VAL GLN TYR GLY GLU ASN VAL THR HIS SEQRES 5 A 193 GLU PHE ASN LEU ASN LYS TYR SER SER THR GLU GLU VAL SEQRES 6 A 193 LEU VAL ALA ALA LYS LYS ILE VAL GLN ARG GLY GLY ALA SEQRES 7 A 193 GLN THR MET THR ALA LEU GLY THR ASP THR ALA ARG LYS SEQRES 8 A 193 GLU ALA PHE THR GLU ALA ARG GLY ALA ARG ARG GLY VAL SEQRES 9 A 193 LYS LYS VAL MET VAL ILE VAL THR ASP GLY GLU SER HIS SEQRES 10 A 193 ASP ASN HIS ARG LEU LYS LYS VAL ILE GLN ASP CYS GLU SEQRES 11 A 193 ASP GLU ASN ILE GLN ARG PHE SER ILE ALA ILE LEU GLY SEQRES 12 A 193 SER TYR ASN ARG GLY ASN LEU SER THR GLU LYS PHE VAL SEQRES 13 A 193 GLU GLU ILE LYS SER ILE ALA SER GLU PRO THR GLU LYS SEQRES 14 A 193 HIS PHE PHE ASN VAL SER ASP GLU LEU ALA LEU VAL THR SEQRES 15 A 193 ILE VAL LYS THR LEU GLY GLU ARG ILE PHE ALA HET MG A 101 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *94(H2 O) HELIX 1 1 PRO A 157 ARG A 171 1 15 HELIX 2 2 SER A 201 ILE A 212 1 12 HELIX 3 3 MET A 221 GLU A 232 1 12 HELIX 4 4 THR A 235 GLY A 239 5 5 HELIX 5 5 ARG A 261 GLU A 272 1 12 HELIX 6 6 LEU A 282 GLY A 288 1 7 HELIX 7 7 THR A 292 ALA A 303 1 12 HELIX 8 8 ASP A 316 THR A 322 5 7 HELIX 9 9 ILE A 323 ALA A 333 1 11 SHEET 1 A 6 VAL A 190 PHE A 194 0 SHEET 2 A 6 GLN A 180 TYR A 186 -1 N ILE A 183 O PHE A 194 SHEET 3 A 6 LEU A 143 ASP A 150 1 O LEU A 143 N GLN A 180 SHEET 4 A 6 LYS A 245 THR A 252 1 O LYS A 245 N ASP A 144 SHEET 5 A 6 ILE A 274 ILE A 281 1 O GLN A 275 N MET A 248 SHEET 6 A 6 PHE A 311 VAL A 314 1 O PHE A 312 N ALA A 280 LINK MG MG A 101 OG SER A 152 1555 1555 2.82 LINK MG MG A 101 OG SER A 154 1555 1555 2.41 LINK MG MG A 101 OD1 ASP A 253 1555 1555 2.64 LINK MG MG A 101 O HOH A 5 1555 1555 2.45 LINK MG MG A 101 O HOH A 47 1555 1555 2.60 LINK MG MG A 101 O HOH A 48 1555 1555 2.54 CISPEP 1 TYR A 156 PRO A 157 0 -0.30 CISPEP 2 GLU A 305 PRO A 306 0 0.57 SITE 1 AC1 6 HOH A 5 HOH A 47 HOH A 48 SER A 152 SITE 2 AC1 6 SER A 154 ASP A 253 CRYST1 74.457 81.858 37.316 90.00 90.78 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 0.013431 0.000000 0.000184 0.00000 SCALE2 0.000000 0.012216 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026801 0.00000