HEADER TRANSFERASE 17-NOV-96 2ABL TITLE SH3-SH2 DOMAIN FRAGMENT OF HUMAN BCR-ABL TYROSINE KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABL TYROSINE KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3-SH2 DOMAIN FRAGMENT; COMPND 5 EC: 2.7.1.112; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: BL21; SOURCE 6 GENE: ABL SH3-SH2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSET; SOURCE 11 EXPRESSION_SYSTEM_GENE: ABL SH3-SH2 KEYWDS TRANSFERASE, TYROSINE KINASE, SH3, SH2, ONCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.-J.NAM,C.A.FREDERICK REVDAT 4 03-APR-24 2ABL 1 REMARK REVDAT 3 14-FEB-24 2ABL 1 REMARK REVDAT 2 24-FEB-09 2ABL 1 VERSN REVDAT 1 04-SEP-97 2ABL 0 JRNL AUTH H.J.NAM,W.G.HASER,T.M.ROBERTS,C.A.FREDERICK JRNL TITL INTRAMOLECULAR INTERACTIONS OF THE REGULATORY DOMAINS OF THE JRNL TITL 2 BCR-ABL KINASE REVEAL A NOVEL CONTROL MECHANISM. JRNL REF STRUCTURE V. 4 1105 1996 JRNL REFN ISSN 0969-2126 JRNL PMID 8805596 JRNL DOI 10.1016/S0969-2126(96)00116-5 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 5575 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE-R REMARK 3 FREE R VALUE TEST SET SELECTION : X-PLOR REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1281 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 40 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 3.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.50 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ABL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177730. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-93 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5585 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 12.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04800 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) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.14000 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE, X-PLOR REMARK 200 STARTING MODEL: ABL SH3, SRC SH2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 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 32.81000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.92500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.81000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.92500 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 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 114 NE2 HIS A 114 CD2 -0.080 REMARK 500 HIS A 148 NE2 HIS A 148 CD2 -0.086 REMARK 500 HIS A 220 NE2 HIS A 220 CD2 -0.077 REMARK 500 HIS A 233 NE2 HIS A 233 CD2 -0.066 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 108 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 TRP A 118 CD1 - CG - CD2 ANGL. DEV. = 5.3 DEGREES REMARK 500 TRP A 118 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 TRP A 118 CG - CD2 - CE3 ANGL. DEV. = 5.9 DEGREES REMARK 500 TRP A 129 CD1 - CG - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 TRP A 129 CB - CG - CD1 ANGL. DEV. = -8.3 DEGREES REMARK 500 TRP A 129 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 TRP A 129 CG - CD2 - CE3 ANGL. DEV. = 5.7 DEGREES REMARK 500 TRP A 146 CD1 - CG - CD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 TRP A 146 CB - CG - CD1 ANGL. DEV. = -9.2 DEGREES REMARK 500 TRP A 146 CE2 - CD2 - CG ANGL. DEV. = -5.9 DEGREES REMARK 500 TRP A 146 CG - CD2 - CE3 ANGL. DEV. = 5.9 DEGREES REMARK 500 HIS A 148 CA - C - N ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG A 153 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 LEU A 169 CA - CB - CG ANGL. DEV. = 22.2 DEGREES REMARK 500 ARG A 180 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 185 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 TYR A 193 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 210 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 VAL A 218 CG1 - CB - CG2 ANGL. DEV. = 10.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 97 -27.87 69.12 REMARK 500 LEU A 169 148.29 -170.80 REMARK 500 SER A 175 -75.00 -76.85 REMARK 500 PRO A 177 -7.30 -58.15 REMARK 500 VAL A 205 -51.19 -122.41 REMARK 500 REMARK 500 REMARK: NULL DBREF 2ABL A 76 237 UNP P00519 ABL1_HUMAN 57 218 SEQRES 1 A 163 MET GLY PRO SER GLU ASN ASP PRO ASN LEU PHE VAL ALA SEQRES 2 A 163 LEU TYR ASP PHE VAL ALA SER GLY ASP ASN THR LEU SER SEQRES 3 A 163 ILE THR LYS GLY GLU LYS LEU ARG VAL LEU GLY TYR ASN SEQRES 4 A 163 HIS ASN GLY GLU TRP CYS GLU ALA GLN THR LYS ASN GLY SEQRES 5 A 163 GLN GLY TRP VAL PRO SER ASN TYR ILE THR PRO VAL ASN SEQRES 6 A 163 SER LEU GLU LYS HIS SER TRP TYR HIS GLY PRO VAL SER SEQRES 7 A 163 ARG ASN ALA ALA GLU TYR LEU LEU SER SER GLY ILE ASN SEQRES 8 A 163 GLY SER PHE LEU VAL ARG GLU SER GLU SER SER PRO GLY SEQRES 9 A 163 GLN ARG SER ILE SER LEU ARG TYR GLU GLY ARG VAL TYR SEQRES 10 A 163 HIS TYR ARG ILE ASN THR ALA SER ASP GLY LYS LEU TYR SEQRES 11 A 163 VAL SER SER GLU SER ARG PHE ASN THR LEU ALA GLU LEU SEQRES 12 A 163 VAL HIS HIS HIS SER THR VAL ALA ASP GLY LEU ILE THR SEQRES 13 A 163 THR LEU HIS TYR PRO ALA PRO FORMUL 2 HOH *40(H2 O) HELIX 1 1 SER A 132 TYR A 134 5 3 HELIX 2 2 LEU A 141 LYS A 143 5 3 HELIX 3 3 ARG A 153 LEU A 159 1 7 HELIX 4 4 LEU A 214 THR A 223 1 10 SHEET 1 A 5 ILE A 135 PRO A 137 0 SHEET 2 A 5 LEU A 84 ALA A 87 -1 N VAL A 86 O THR A 136 SHEET 3 A 5 LYS A 106 TYR A 112 -1 N LEU A 107 O PHE A 85 SHEET 4 A 5 TRP A 118 THR A 123 -1 N GLN A 122 O ARG A 108 SHEET 5 A 5 GLY A 126 PRO A 131 -1 N VAL A 130 O CYS A 119 SHEET 1 B 3 PHE A 168 GLU A 172 0 SHEET 2 B 3 ARG A 180 TYR A 186 -1 N SER A 183 O LEU A 169 SHEET 3 B 3 ARG A 189 ILE A 195 -1 N ILE A 195 O ARG A 180 CRYST1 65.620 45.850 54.450 90.00 95.18 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 0.015239 0.000000 0.001382 0.00000 SCALE2 0.000000 0.021810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018441 0.00000