HEADER PROTEIN BINDING 05-OCT-21 7PVQ TITLE CRYSTAL STRUCTURE OF THE ABL SH3 DOMAIN V73E-A74S-S75R-G76T-D77E-G92N- TITLE 2 Y93N-N94T-H95E MUTANT IN THE SPACE GROUP P21221 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE ABL1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 1,ABELSON COMPND 5 TYROSINE-PROTEIN KINASE 1,PROTO-ONCOGENE C-ABL,P150; 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 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: PHTP1 KEYWDS BETA BARREL, SH3 DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS,M.C.SALINAS GARCIA REVDAT 2 31-JAN-24 7PVQ 1 REMARK REVDAT 1 14-SEP-22 7PVQ 0 JRNL AUTH A.CAMARA-ARTIGAS,M.C.SALINAS GARCIA JRNL TITL THE EFFECT OF THE HINGE LOOPS COMPOSITION IN THE DOMAIN JRNL TITL 2 SWAPPING OF THE SH3 DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.9 REMARK 3 NUMBER OF REFLECTIONS : 25295 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1203 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 19.7600 - 3.2200 0.81 2734 119 0.2120 0.2464 REMARK 3 2 3.2200 - 2.5600 0.85 2812 149 0.2382 0.3001 REMARK 3 3 2.5600 - 2.2400 0.79 2624 153 0.2335 0.2700 REMARK 3 4 2.2300 - 2.0300 0.76 2562 131 0.2126 0.2385 REMARK 3 5 2.0300 - 1.8900 0.71 2346 126 0.2473 0.3035 REMARK 3 6 1.8900 - 1.7700 0.83 2791 152 0.2369 0.2431 REMARK 3 7 1.7700 - 1.6900 0.86 2861 134 0.2541 0.2994 REMARK 3 8 1.6900 - 1.6100 0.86 2903 133 0.2561 0.3542 REMARK 3 9 1.6100 - 1.5500 0.73 2459 106 0.2705 0.2916 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.55 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7PVQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1292118430. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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) : 0.97910 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15097 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 19.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 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: 3EG3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULFATE, 0.1M MES, PH REMARK 280 6.0, VAPOR DIFFUSION, SITTING 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 13.65650 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.42700 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 13.65650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.42700 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 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 B 242 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 GLY A 62 REMARK 465 GLY B 62 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 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 77 CG CD OE1 OE2 REMARK 470 GLU B 77 CG CD OE1 OE2 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 64 30.39 -150.45 REMARK 500 ASN A 78 13.73 80.39 REMARK 500 ASN B 64 29.99 -152.02 REMARK 500 ASN B 78 9.97 83.30 REMARK 500 REMARK 500 REMARK: NULL DBREF 7PVQ A 63 120 UNP P00519 ABL1_HUMAN 63 120 DBREF 7PVQ B 63 120 UNP P00519 ABL1_HUMAN 63 120 SEQADV 7PVQ GLY A 62 UNP P00519 EXPRESSION TAG SEQADV 7PVQ GLU A 73 UNP P00519 VAL 73 ENGINEERED MUTATION SEQADV 7PVQ SER A 74 UNP P00519 ALA 74 ENGINEERED MUTATION SEQADV 7PVQ ARG A 75 UNP P00519 SER 75 ENGINEERED MUTATION SEQADV 7PVQ THR A 76 UNP P00519 GLY 76 ENGINEERED MUTATION SEQADV 7PVQ GLU A 77 UNP P00519 ASP 77 ENGINEERED MUTATION SEQADV 7PVQ ASN A 92 UNP P00519 GLY 92 ENGINEERED MUTATION SEQADV 7PVQ ASN A 93 UNP P00519 TYR 93 ENGINEERED MUTATION SEQADV 7PVQ THR A 94 UNP P00519 ASN 94 ENGINEERED MUTATION SEQADV 7PVQ GLU A 95 UNP P00519 HIS 95 ENGINEERED MUTATION SEQADV 7PVQ GLY B 62 UNP P00519 EXPRESSION TAG SEQADV 7PVQ GLU B 73 UNP P00519 VAL 73 ENGINEERED MUTATION SEQADV 7PVQ SER B 74 UNP P00519 ALA 74 ENGINEERED MUTATION SEQADV 7PVQ ARG B 75 UNP P00519 SER 75 ENGINEERED MUTATION SEQADV 7PVQ THR B 76 UNP P00519 GLY 76 ENGINEERED MUTATION SEQADV 7PVQ GLU B 77 UNP P00519 ASP 77 ENGINEERED MUTATION SEQADV 7PVQ ASN B 92 UNP P00519 GLY 92 ENGINEERED MUTATION SEQADV 7PVQ ASN B 93 UNP P00519 TYR 93 ENGINEERED MUTATION SEQADV 7PVQ THR B 94 UNP P00519 ASN 94 ENGINEERED MUTATION SEQADV 7PVQ GLU B 95 UNP P00519 HIS 95 ENGINEERED MUTATION SEQRES 1 A 59 GLY PRO ASN LEU PHE VAL ALA LEU TYR ASP PHE GLU SER SEQRES 2 A 59 ARG THR GLU ASN THR LEU SER ILE THR LYS GLY GLU LYS SEQRES 3 A 59 LEU ARG VAL LEU ASN ASN THR GLU ASN GLY GLU TRP CYS SEQRES 4 A 59 GLU ALA GLN THR LYS ASN GLY GLN GLY TRP VAL PRO SER SEQRES 5 A 59 ASN TYR ILE THR PRO VAL ASN SEQRES 1 B 59 GLY PRO ASN LEU PHE VAL ALA LEU TYR ASP PHE GLU SER SEQRES 2 B 59 ARG THR GLU ASN THR LEU SER ILE THR LYS GLY GLU LYS SEQRES 3 B 59 LEU ARG VAL LEU ASN ASN THR GLU ASN GLY GLU TRP CYS SEQRES 4 B 59 GLU ALA GLN THR LYS ASN GLY GLN GLY TRP VAL PRO SER SEQRES 5 B 59 ASN TYR ILE THR PRO VAL ASN FORMUL 3 HOH *147(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 ALA A 102 O GLY A 109 SHEET 3 AA1 5 LYS A 87 ASN 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 ALA B 102 O GLY B 109 SHEET 3 AA2 5 LYS B 87 ASN B 93 -1 N LEU B 91 O GLU B 101 SHEET 4 AA2 5 LEU B 65 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 CRYST1 27.313 43.465 94.854 90.00 90.00 90.00 P 21 2 21 8 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 0.036612 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023007 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010543 0.00000