HEADER PROTEIN BINDING 05-OCT-21 7PW2 TITLE CRYSTAL STRUCTURE OF THE ABL SH3 DOMAIN V73E-A74S-S75R-G76T-D77E TITLE 2 MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-SPECIFIC PROTEIN-TYROSINE KINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.10.2; COMPND 5 ENGINEERED: YES; COMPND 6 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: BCR/ABL FUSION; 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 7PW2 1 REMARK REVDAT 1 14-SEP-22 7PW2 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. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.4 REMARK 3 NUMBER OF REFLECTIONS : 32715 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.360 REMARK 3 FREE R VALUE TEST SET COUNT : 1752 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 17.4400 - 2.5800 0.72 2275 128 0.1615 0.1965 REMARK 3 2 2.5800 - 2.0500 0.74 2300 155 0.1789 0.1959 REMARK 3 3 2.0500 - 1.7900 0.75 2396 123 0.1929 0.1709 REMARK 3 4 1.7900 - 1.6300 0.76 2460 88 0.1955 0.1769 REMARK 3 5 1.6300 - 1.5100 0.74 2286 168 0.2107 0.2319 REMARK 3 6 1.5100 - 1.4200 0.78 2478 141 0.2197 0.1916 REMARK 3 7 1.4200 - 1.3500 0.75 2371 141 0.1975 0.2399 REMARK 3 8 1.3500 - 1.2900 0.76 2390 129 0.1934 0.2663 REMARK 3 9 1.2900 - 1.2400 0.77 2418 123 0.2188 0.2244 REMARK 3 10 1.2400 - 1.2000 0.76 2404 150 0.2295 0.2420 REMARK 3 11 1.2000 - 1.1600 0.76 2372 119 0.2194 0.2638 REMARK 3 12 1.1600 - 1.1300 0.75 2401 135 0.2495 0.2688 REMARK 3 13 1.1300 - 1.1000 0.76 2412 152 0.2785 0.3269 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.52 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 7PW2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1292118452. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.97924 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 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21193 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 17.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.45500 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 (%): 40.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, 0.1M HEPES, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 15.20350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 7.60175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.80525 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 61 REMARK 465 GLY A 62 REMARK 465 ASN A 120 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 ASN A 64 CG OD1 ND2 REMARK 470 LEU A 65 CG CD1 CD2 REMARK 470 GLU A 73 CG CD OE1 OE2 REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 470 THR A 76 OG1 CG2 REMARK 470 GLU A 77 CG CD OE1 OE2 REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 95 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 98 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 -31.04 -131.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 7PW2 A 63 120 UNP A9UF07 A9UF07_HUMAN 723 780 SEQADV 7PW2 GLY A 61 UNP A9UF07 EXPRESSION TAG SEQADV 7PW2 GLY A 62 UNP A9UF07 EXPRESSION TAG SEQADV 7PW2 GLU A 73 UNP A9UF07 VAL 733 ENGINEERED MUTATION SEQADV 7PW2 SER A 74 UNP A9UF07 ALA 734 ENGINEERED MUTATION SEQADV 7PW2 ARG A 75 UNP A9UF07 SER 735 ENGINEERED MUTATION SEQADV 7PW2 THR A 76 UNP A9UF07 GLY 736 ENGINEERED MUTATION SEQADV 7PW2 GLU A 77 UNP A9UF07 ASP 737 ENGINEERED MUTATION SEQRES 1 A 60 GLY GLY PRO ASN LEU PHE VAL ALA LEU TYR ASP PHE GLU SEQRES 2 A 60 SER ARG THR GLU ASN THR LEU SER ILE THR LYS GLY GLU SEQRES 3 A 60 LYS LEU ARG VAL LEU GLY TYR ASN HIS ASN GLY GLU TRP SEQRES 4 A 60 CYS GLU ALA GLN THR LYS ASN GLY GLN GLY TRP VAL PRO SEQRES 5 A 60 SER ASN TYR ILE THR PRO VAL ASN FORMUL 2 HOH *51(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 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 CRYST1 42.580 42.580 30.407 90.00 90.00 90.00 P 41 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 0.023485 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023485 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032887 0.00000