HEADER TRANSFERASE 25-JUN-17 5OAZ TITLE CRYSTAL STRUCTURE OF THE ABL-SH3 DOMAIN AT PH 7.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE ABL1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SH3 DOMAIN; COMPND 5 SYNONYM: ABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 1,ABELSON COMPND 6 TYROSINE-PROTEIN KINASE 1,PROTO-ONCOGENE C-ABL,P150; COMPND 7 EC: 2.7.10.2; COMPND 8 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: ABL1, ABL, JTK7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS BETA SHANDWICH, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS REVDAT 4 17-JAN-24 5OAZ 1 REMARK REVDAT 3 24-JAN-18 5OAZ 1 SOURCE REVDAT 2 13-SEP-17 5OAZ 1 REMARK REVDAT 1 12-JUL-17 5OAZ 0 JRNL AUTH A.CAMARA-ARTIGAS JRNL TITL CRYSTAL STRUCTURE OF THE ABL-SH3 DOMAIN AT PH 7.5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 118361 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.250 REMARK 3 FREE R VALUE TEST SET COUNT : 6209 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 19.9784 - 3.1962 0.99 3874 190 0.1701 0.1961 REMARK 3 2 3.1962 - 2.5386 1.00 3916 252 0.1717 0.1867 REMARK 3 3 2.5386 - 2.2182 0.99 3914 204 0.1513 0.1885 REMARK 3 4 2.2182 - 2.0156 0.99 3808 298 0.1330 0.1325 REMARK 3 5 2.0156 - 1.8712 0.99 3838 228 0.1226 0.1549 REMARK 3 6 1.8712 - 1.7610 0.98 3854 198 0.1280 0.1436 REMARK 3 7 1.7610 - 1.6728 0.98 3890 184 0.1221 0.1273 REMARK 3 8 1.6728 - 1.6000 0.98 3759 242 0.1116 0.1287 REMARK 3 9 1.6000 - 1.5385 0.97 3796 322 0.1093 0.1243 REMARK 3 10 1.5385 - 1.4854 0.97 3784 218 0.1028 0.1429 REMARK 3 11 1.4854 - 1.4390 0.96 3762 172 0.1109 0.1301 REMARK 3 12 1.4390 - 1.3978 0.97 3854 148 0.1060 0.1165 REMARK 3 13 1.3978 - 1.3610 0.97 3800 258 0.1031 0.1190 REMARK 3 14 1.3610 - 1.3278 0.95 3834 150 0.1062 0.1304 REMARK 3 15 1.3278 - 1.2977 0.95 3698 216 0.1052 0.1343 REMARK 3 16 1.2977 - 1.2701 0.94 3676 174 0.1067 0.1353 REMARK 3 17 1.2701 - 1.2446 0.95 3736 184 0.1138 0.1126 REMARK 3 18 1.2446 - 1.2212 0.94 3699 176 0.1190 0.1473 REMARK 3 19 1.2212 - 1.1994 0.94 3806 134 0.1218 0.1625 REMARK 3 20 1.1994 - 1.1790 0.95 3681 242 0.1262 0.1702 REMARK 3 21 1.1790 - 1.1600 0.94 3537 232 0.1360 0.1599 REMARK 3 22 1.1600 - 1.1422 0.93 3750 230 0.1424 0.1608 REMARK 3 23 1.1422 - 1.1254 0.94 3634 216 0.1433 0.1526 REMARK 3 24 1.1254 - 1.1095 0.92 3633 182 0.1594 0.1850 REMARK 3 25 1.1095 - 1.0945 0.92 3549 285 0.1753 0.1785 REMARK 3 26 1.0945 - 1.0803 0.92 3607 222 0.1903 0.2246 REMARK 3 27 1.0803 - 1.0668 0.92 3491 286 0.2083 0.2142 REMARK 3 28 1.0668 - 1.0540 0.92 3781 90 0.2211 0.2438 REMARK 3 29 1.0540 - 1.0417 0.91 3586 124 0.2451 0.2632 REMARK 3 30 1.0417 - 1.0300 0.89 3605 152 0.2889 0.2730 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.56 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 : 0.010 930 REMARK 3 ANGLE : 1.114 1267 REMARK 3 CHIRALITY : 0.095 136 REMARK 3 PLANARITY : 0.007 165 REMARK 3 DIHEDRAL : 12.863 313 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 5OAZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005497. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-15 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL-CUT CRYSTAL REMARK 200 MONOCHROMATOR AND A PAIR OF KB REMARK 200 MIRRORS REMARK 200 OPTICS : CHANNEL-CUT SI(111) REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 118361 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.030 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.59200 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: PHASER REMARK 200 STARTING MODEL: 4JJB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.65 M AMMONIUM SULPHATE, 0.1 M HEPES REMARK 280 AND 6% PEG 300, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 30.03067 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 15.01533 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 MET A 59 REMARK 465 GLU A 60 REMARK 465 ASN A 61 REMARK 465 SER A 121 REMARK 465 MET B 59 REMARK 465 GLU B 60 REMARK 465 ASN B 61 REMARK 465 ASP B 62 REMARK 465 PRO B 63 REMARK 465 ASN B 64 REMARK 465 SER B 121 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 ASP A 62 CG OD1 OD2 REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 105 CG CD CE NZ REMARK 470 LEU B 65 CG CD1 CD2 REMARK 470 ARG B 89 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 105 CG CD CE NZ 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 -80.50 -105.48 REMARK 500 SER B 75 -81.82 -104.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 360 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH B 364 DISTANCE = 5.87 ANGSTROMS 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 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 202 DBREF 5OAZ A 60 121 UNP P00519 ABL1_HUMAN 79 140 DBREF 5OAZ B 60 121 UNP P00519 ABL1_HUMAN 79 140 SEQADV 5OAZ MET A 59 UNP P00519 INITIATING METHIONINE SEQADV 5OAZ MET B 59 UNP P00519 INITIATING METHIONINE 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 SEQRES 1 B 63 MET GLU ASN ASP PRO ASN LEU PHE VAL ALA LEU TYR ASP SEQRES 2 B 63 PHE VAL ALA SER GLY ASP ASN THR LEU SER ILE THR LYS SEQRES 3 B 63 GLY GLU LYS LEU ARG VAL LEU GLY TYR ASN HIS ASN GLY SEQRES 4 B 63 GLU TRP CYS GLU ALA GLN THR LYS ASN GLY GLN GLY TRP SEQRES 5 B 63 VAL PRO SER ASN TYR ILE THR PRO VAL ASN SER HET PEG A 201 17 HET PEG B 201 17 HET PEG B 202 17 HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 3 PEG 3(C4 H10 O3) FORMUL 6 HOH *124(H2 O) SHEET 1 AA1 5 GLY A 107 PRO A 112 0 SHEET 2 AA1 5 TRP A 99 THR A 104 -1 N CYS A 100 O VAL A 111 SHEET 3 AA1 5 LYS A 87 TYR A 93 -1 N LEU A 91 O GLU A 101 SHEET 4 AA1 5 LEU A 65 ALA A 68 -1 N PHE A 66 O LEU A 88 SHEET 5 AA1 5 ILE A 116 PRO A 118 -1 O THR A 117 N VAL A 67 SHEET 1 AA2 5 GLY B 107 PRO B 112 0 SHEET 2 AA2 5 TRP B 99 THR B 104 -1 N CYS B 100 O VAL B 111 SHEET 3 AA2 5 LYS B 87 TYR B 93 -1 N LEU B 91 O GLU B 101 SHEET 4 AA2 5 PHE B 66 ALA B 68 -1 N PHE B 66 O LEU B 88 SHEET 5 AA2 5 ILE B 116 PRO B 118 -1 O THR B 117 N VAL B 67 SITE 1 AC1 3 TRP A 99 HOH A 340 HOH A 343 SITE 1 AC2 1 HOH B 328 SITE 1 AC3 3 TYR A 93 GLY A 97 GLY B 97 CRYST1 49.919 49.919 45.046 90.00 90.00 120.00 P 32 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 0.020033 0.011566 0.000000 0.00000 SCALE2 0.000000 0.023132 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022200 0.00000