HEADER TRANSFERASE 12-MAR-09 3GM3 TITLE CRYSTAL STRUCTURE OF THE FOCAL ADHESION TARGETING (FAT) DOMAIN OF PYK2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN TYROSINE KINASE 2 BETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FOCAL ADHESION TARGETING (FAT) DOMAIN, UNP RESIDUES 861- COMPND 5 1009; COMPND 6 EC: 2.7.10.2; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS FOUR-HELIX BUNDLE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.E.LULO,S.YUZAWA,J.SCHLESSINGER REVDAT 4 01-NOV-23 3GM3 1 REMARK REVDAT 3 10-NOV-21 3GM3 1 SEQADV REVDAT 2 16-JUN-09 3GM3 1 JRNL REVDAT 1 05-MAY-09 3GM3 0 JRNL AUTH J.LULO,S.YUZAWA,J.SCHLESSINGER JRNL TITL CRYSTAL STRUCTURES OF FREE AND LIGAND-BOUND FOCAL ADHESION JRNL TITL 2 TARGETING DOMAIN OF PYK2 JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 383 347 2009 JRNL REFN ISSN 0006-291X JRNL PMID 19358827 JRNL DOI 10.1016/J.BBRC.2009.04.011 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0066 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 5186 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 + TEST SET) : 0.256 REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 232 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 294 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 17 REMARK 3 BIN FREE R VALUE : 0.4530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 997 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 14 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.22000 REMARK 3 B22 (A**2) : 1.23000 REMARK 3 B33 (A**2) : -1.45000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.704 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.345 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.257 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.447 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.894 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1003 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1365 ; 1.216 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 132 ; 5.304 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 39 ;36.457 ;26.154 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 184 ;22.577 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;17.608 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 179 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 716 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 664 ; 0.910 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1067 ; 1.345 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 339 ; 1.379 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 298 ; 2.512 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3GM3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052030. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5467 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3GM2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 100MM HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 14.23100 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.75100 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 14.23100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 64.75100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 857 REMARK 465 SER A 858 REMARK 465 HIS A 859 REMARK 465 MET A 860 REMARK 465 ARG A 861 REMARK 465 LEU A 862 REMARK 465 GLY A 863 REMARK 465 ALA A 864 REMARK 465 GLN A 865 REMARK 465 SER A 866 REMARK 465 ILE A 867 REMARK 465 GLN A 868 REMARK 465 PRO A 869 REMARK 465 THR A 870 REMARK 465 ALA A 871 REMARK 465 HIS A 1005 REMARK 465 PRO A 1006 REMARK 465 PRO A 1007 REMARK 465 ALA A 1008 REMARK 465 GLU A 1009 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 895 CG CD CE NZ REMARK 470 GLU A 897 CG CD OE1 OE2 REMARK 470 GLU A 904 CG CD OE1 OE2 REMARK 470 LYS A 911 CG CD CE NZ REMARK 470 GLU A 938 CG CD OE1 OE2 REMARK 470 LYS A 944 CG CD CE NZ REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GM1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE FOCAL ADHESION TARGETING (FAT) DOMAIN OF REMARK 900 PYK2 IN COMPLEX WITH PAXILLIN LD4 MOTIF-DERIVED PEPTIDES REMARK 900 RELATED ID: 3GM2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE FOCAL ADHESION TARGETING (FAT) DOMAIN OF REMARK 900 PYK2 DBREF 3GM3 A 861 1009 UNP Q14289 FAK2_HUMAN 861 1009 SEQADV 3GM3 GLY A 857 UNP Q14289 EXPRESSION TAG SEQADV 3GM3 SER A 858 UNP Q14289 EXPRESSION TAG SEQADV 3GM3 HIS A 859 UNP Q14289 EXPRESSION TAG SEQADV 3GM3 MET A 860 UNP Q14289 EXPRESSION TAG SEQADV 3GM3 ALA A 899 UNP Q14289 CYS 899 ENGINEERED MUTATION SEQRES 1 A 153 GLY SER HIS MET ARG LEU GLY ALA GLN SER ILE GLN PRO SEQRES 2 A 153 THR ALA ASN LEU ASP ARG THR ASP ASP LEU VAL TYR LEU SEQRES 3 A 153 ASN VAL MET GLU LEU VAL ARG ALA VAL LEU GLU LEU LYS SEQRES 4 A 153 ASN GLU LEU ALA GLN LEU PRO PRO GLU GLY TYR VAL VAL SEQRES 5 A 153 VAL VAL LYS ASN VAL GLY LEU THR LEU ARG LYS LEU ILE SEQRES 6 A 153 GLY SER VAL ASP ASP LEU LEU PRO SER LEU PRO SER SER SEQRES 7 A 153 SER ARG THR GLU ILE GLU GLY THR GLN LYS LEU LEU ASN SEQRES 8 A 153 LYS ASP LEU ALA GLU LEU ILE ASN LYS MET ARG LEU ALA SEQRES 9 A 153 GLN GLN ASN ALA VAL THR SER LEU SER GLU GLU CYS LYS SEQRES 10 A 153 ARG GLN MET LEU THR ALA SER HIS THR LEU ALA VAL ASP SEQRES 11 A 153 ALA LYS ASN LEU LEU ASP ALA VAL ASP GLN ALA LYS VAL SEQRES 12 A 153 LEU ALA ASN LEU ALA HIS PRO PRO ALA GLU FORMUL 2 HOH *14(H2 O) HELIX 1 1 ASP A 878 LEU A 898 1 21 HELIX 2 2 ALA A 899 LEU A 901 5 3 HELIX 3 3 PRO A 902 LEU A 928 1 27 HELIX 4 4 PRO A 929 LEU A 931 5 3 HELIX 5 5 PRO A 932 ASN A 963 1 32 HELIX 6 6 LEU A 968 ALA A 1004 1 37 CRYST1 28.462 42.791 129.502 90.00 90.00 90.00 P 21 2 21 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 0.035135 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023369 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007722 0.00000