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
(ATOM LINES ARE NOT SHOWN.)
END
