HEADER TRANSFERASE 07-MAR-13 4JJB TITLE CRYSTAL STRUCTURE OF THE ABL-SH3 DOMAIN AT PH3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE ABL1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3 DOMAIN, UNP RESIDUES 60-121; COMPND 5 SYNONYM: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1, ABELSON MURINE COMPND 6 LEUKEMIA VIRAL ONCOGENE HOMOLOG 1, ABELSON TYROSINE-PROTEIN KINASE 1, COMPND 7 PROTO-ONCOGENE C-ABL, P150; COMPND 8 EC: 2.7.10.2; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ABL, ABL1, JTK7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS BETA SHANDWICH, SH3 DOMAIN, KINASE, POLY PROLINE RICH MOTIFS, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS,J.M.MARTIN-GARCIA REVDAT 2 08-NOV-23 4JJB 1 REMARK SEQADV REVDAT 1 12-MAR-14 4JJB 0 JRNL AUTH A.CAMARA-ARTIGAS,J.M.MARTIN-GARCIA JRNL TITL CRYSTAL STRUCTURE OF THE ABL-SH3 DOMAIN AT PH3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.CAMARA-ARTIGAS,A.PALENCIA,J.C.MARTINEZ,I.LUQUE,J.A.GAVIRA, REMARK 1 AUTH 2 J.M.GARCIA-RUIZ REMARK 1 TITL CRYSTALLIZATION BY CAPILLARY COUNTER-DIFFUSION AND STRUCTURE REMARK 1 TITL 2 DETERMINATION OF THE N114A MUTANT OF THE SH3 DOMAIN OF ABL REMARK 1 TITL 3 TYROSINE KINASE COMPLEXED WITH A HIGH-AFFINITY PEPTIDE REMARK 1 TITL 4 LIGAND REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 63 646 2007 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 17452790 REMARK 1 DOI 10.1107/S0907444907011109 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.PALENCIA,A.CAMARA-ARTIGAS,M.T.PISABARRO,J.C.MARTINEZ, REMARK 1 AUTH 2 I.LUQUE REMARK 1 TITL ROLE OF INTERFACIAL WATER MOLECULES IN PROLINE-RICH LIGAND REMARK 1 TITL 2 RECOGNITION BY THE SRC HOMOLOGY 3 DOMAIN OF ABL REMARK 1 REF J.BIOL.CHEM. V. 285 2823 2010 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 19906645 REMARK 1 DOI 10.1074/JBC.M109.048033 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 7854 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.620 REMARK 3 FREE R VALUE TEST SET COUNT : 363 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 16.5200 - 2.3800 0.98 2550 121 0.1732 0.2501 REMARK 3 2 2.3800 - 1.8900 0.98 2501 124 0.1674 0.1792 REMARK 3 3 1.8900 - 1.6500 0.97 2440 118 0.1250 0.2149 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.10 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 478 REMARK 3 ANGLE : 1.071 647 REMARK 3 CHIRALITY : 0.060 68 REMARK 3 PLANARITY : 0.005 82 REMARK 3 DIHEDRAL : 12.927 169 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4JJB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078117. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : CHANNEL CUT ESRF MONOCHROMATOR REMARK 200 OPTICS : TORODIAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7859 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 43.708 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.13900 REMARK 200 R SYM (I) : 0.13900 REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.14100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3EG3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3M AMMONIUM SULPHATE, 5% PEG 200, REMARK 280 0.05M GLYCINE, CAPILLARY COUNTERDIFFUSION, TEMPERATURE 298K, PH 3 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -Y,-X,-Z+1/3 REMARK 290 5555 -X+Y,Y,-Z+2/3 REMARK 290 6555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.08000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.04000 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 15.04000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.08000 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 302 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 325 LIES ON A SPECIAL POSITION. 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 MET A 59 REMARK 465 GLU A 60 REMARK 465 ASN A 61 REMARK 465 ASP A 62 REMARK 465 PRO A 63 REMARK 465 SER A 121 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 SER A 75 -70.75 -133.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ABQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE UNLIGANDED ABL TYROSINE KINASE SH3 DOMAIN REMARK 900 RELATED ID: 3EG0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N114T MUTANT OF ABL-SH3 DOMAIN PH 3 REMARK 900 RELATED ID: 3EG2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N114Q MUTANT OF ABL-SH3 DOMAIN REMARK 900 RELATED ID: 3EGU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N114A MUTANT OF ABL-SH3 DOMAIN PH7 REMARK 900 RELATED ID: 4JJC RELATED DB: PDB REMARK 900 RELATED ID: 4JJD RELATED DB: PDB DBREF 4JJB A 60 121 UNP P00519 ABL1_HUMAN 60 121 SEQADV 4JJB MET A 59 UNP P00519 EXPRESSION TAG SEQRES 1 A 63 MET GLU ASN ASP PRO ASN LEU PHE VAL ALA LEU TYR ASP SEQRES 2 A 63 PHE VAL ALA SER GLY ASP ASN THR LEU SER ILE THR LYS SEQRES 3 A 63 GLY GLU LYS LEU ARG VAL LEU GLY TYR ASN HIS ASN GLY SEQRES 4 A 63 GLU TRP CYS GLU ALA GLN THR LYS ASN GLY GLN GLY TRP SEQRES 5 A 63 VAL PRO SER ASN TYR ILE THR PRO VAL ASN SER HET PEG A 201 7 HET PEG A 202 7 HET SO4 A 203 5 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM SO4 SULFATE ION FORMUL 2 PEG 2(C4 H10 O3) FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *35(H2 O) SHEET 1 A 5 GLY A 107 PRO A 112 0 SHEET 2 A 5 TRP A 99 THR A 104 -1 N CYS A 100 O VAL A 111 SHEET 3 A 5 LYS A 87 TYR A 93 -1 N LEU A 91 O GLU A 101 SHEET 4 A 5 LEU A 65 ALA A 68 -1 N PHE A 66 O LEU A 88 SHEET 5 A 5 ILE A 116 PRO A 118 -1 O THR A 117 N VAL A 67 SITE 1 AC1 2 TRP A 110 HOH A 331 SITE 1 AC2 3 LEU A 91 TYR A 93 GLU A 101 SITE 1 AC3 4 GLU A 86 LYS A 87 LYS A 105 HOH A 316 CRYST1 50.470 50.470 45.120 90.00 90.00 120.00 P 32 1 2 6 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 0.019814 0.011440 0.000000 0.00000 SCALE2 0.000000 0.022879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022163 0.00000