PDB Short entry for 1QCY 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 5 14-FEB-24 1QCY 1 REMARK LINK 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 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) : 23.10 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 DEPOSITION ID IS D_1000009087. 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 <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) : 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 <I/SIGMA(I)> 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 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 HOH A 5 O REMARK 620 2 HOH A 47 O 96.5 REMARK 620 3 HOH A 48 O 114.3 86.0 REMARK 620 4 SER A 152 OG 71.1 160.9 112.2 REMARK 620 5 SER A 154 OG 146.3 95.6 97.9 88.0 REMARK 620 6 ASP A 253 OD1 70.4 90.9 174.7 71.4 78.1 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 O HOH A 5 MG MG A 101 1555 1555 2.45 LINK O HOH A 47 MG MG A 101 1555 1555 2.60 LINK O HOH A 48 MG MG A 101 1555 1555 2.54 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 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