HEADER HYDROLASE 09-OCT-18 6MQG TITLE CRYSTAL STRUCTURE OF KRAS V14I-GDP DEMONSTRATING OPEN SWITCH 1 TITLE 2 CONFORMATION - FORM 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE KRAS; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: K-RAS 2,KI-RAS,C-K-RAS,C-KI-RAS; COMPND 5 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: KRAS, KRAS2, RASK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GTPASE KRAS HYDROLYSIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,K.D.WESTOVER REVDAT 5 15-NOV-23 6MQG 1 REMARK REVDAT 4 11-OCT-23 6MQG 1 REMARK REVDAT 3 02-OCT-19 6MQG 1 JRNL REVDAT 2 07-AUG-19 6MQG 1 JRNL REVDAT 1 31-JUL-19 6MQG 0 JRNL AUTH A.K.BERA,J.LU,T.E.WALES,S.GONDI,D.GURBANI,A.NELSON, JRNL AUTH 2 J.R.ENGEN,K.D.WESTOVER JRNL TITL STRUCTURAL BASIS OF THE ATYPICAL ACTIVATION MECHANISM OF JRNL TITL 2 KRASV14I. JRNL REF J.BIOL.CHEM. V. 294 13964 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31341022 JRNL DOI 10.1074/JBC.RA119.009131 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14RC3_3199 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 31214 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1527 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 28.8500 - 3.3300 1.00 2892 126 0.1510 0.1854 REMARK 3 2 3.3300 - 2.6500 1.00 2784 126 0.1549 0.1686 REMARK 3 3 2.6500 - 2.3100 1.00 2757 133 0.1428 0.1711 REMARK 3 4 2.3100 - 2.1000 0.97 2577 195 0.1799 0.2361 REMARK 3 5 2.1000 - 1.9500 0.99 2668 150 0.1448 0.1727 REMARK 3 6 1.9500 - 1.8300 0.94 2603 113 0.2325 0.2837 REMARK 3 7 1.8300 - 1.7400 1.00 2673 153 0.1367 0.1889 REMARK 3 8 1.7400 - 1.6700 1.00 2716 137 0.1314 0.2035 REMARK 3 9 1.6700 - 1.6000 1.00 2693 139 0.1258 0.1712 REMARK 3 10 1.6000 - 1.5500 1.00 2712 131 0.1261 0.1677 REMARK 3 11 1.5500 - 1.5000 0.96 2612 124 0.1361 0.2237 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) : 0.119 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.062 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.26 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 : 0.004 1460 REMARK 3 ANGLE : 0.653 1986 REMARK 3 CHIRALITY : 0.060 222 REMARK 3 PLANARITY : 0.004 269 REMARK 3 DIHEDRAL : 22.367 592 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 6MQG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237404. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31559 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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: 4OBE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M NA/K PHOSPHATE, PH 8.2, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z 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 0.00000 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 0.00000 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 0.00000 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 0.00000 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 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 482 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 486 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 493 LIES ON A SPECIAL POSITION. 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 39 1.08 80.13 REMARK 500 LYS A 117 33.82 71.12 REMARK 500 ARG A 149 -5.75 82.28 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 493 DISTANCE = 6.94 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 201 DBREF 6MQG A 3 169 UNP P01116 RASK_HUMAN 3 169 SEQADV 6MQG ILE A 14 UNP P01116 VAL 14 ENGINEERED MUTATION SEQRES 1 A 167 GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY GLY ILE GLY SEQRES 2 A 167 LYS SER ALA LEU THR ILE GLN LEU ILE GLN ASN HIS PHE SEQRES 3 A 167 VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SER TYR ARG SEQRES 4 A 167 LYS GLN VAL VAL ILE ASP GLY GLU THR CYS LEU LEU ASP SEQRES 5 A 167 ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SER ALA MET SEQRES 6 A 167 ARG ASP GLN TYR MET ARG THR GLY GLU GLY PHE LEU CYS SEQRES 7 A 167 VAL PHE ALA ILE ASN ASN THR LYS SER PHE GLU ASP ILE SEQRES 8 A 167 HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL LYS ASP SER SEQRES 9 A 167 GLU ASP VAL PRO MET VAL LEU VAL GLY ASN LYS CSO ASP SEQRES 10 A 167 LEU PRO SER ARG THR VAL ASP THR LYS GLN ALA GLN ASP SEQRES 11 A 167 LEU ALA ARG SER TYR GLY ILE PRO PHE ILE GLU THR SER SEQRES 12 A 167 ALA LYS THR ARG GLN GLY VAL ASP ASP ALA PHE TYR THR SEQRES 13 A 167 LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU LYS MODRES 6MQG CSO A 118 CYS MODIFIED RESIDUE HET CSO A 118 12 HET GDP A 201 43 HETNAM CSO S-HYDROXYCYSTEINE HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 HOH *193(H2 O) HELIX 1 AA1 GLY A 15 HIS A 27 1 13 HELIX 2 AA2 ALA A 59 SER A 65 5 7 HELIX 3 AA3 MET A 67 GLY A 75 1 9 HELIX 4 AA4 ASN A 86 ASP A 92 1 7 HELIX 5 AA5 ASP A 92 ASP A 105 1 14 HELIX 6 AA6 ASP A 126 GLY A 138 1 13 HELIX 7 AA7 GLY A 151 LYS A 169 1 19 SHEET 1 AA1 7 PHE A 28 TYR A 32 0 SHEET 2 AA1 7 TYR A 40 ILE A 46 -1 O ARG A 41 N GLU A 31 SHEET 3 AA1 7 GLU A 49 LEU A 56 -1 O GLU A 49 N ILE A 46 SHEET 4 AA1 7 TYR A 4 VAL A 9 1 N VAL A 8 O LEU A 56 SHEET 5 AA1 7 GLY A 77 ALA A 83 1 O VAL A 81 N VAL A 9 SHEET 6 AA1 7 MET A 111 ASN A 116 1 O ASN A 116 N PHE A 82 SHEET 7 AA1 7 PHE A 141 GLU A 143 1 O ILE A 142 N LEU A 113 LINK C LYS A 117 N CSO A 118 1555 1555 1.33 LINK C CSO A 118 N ASP A 119 1555 1555 1.33 SITE 1 AC1 25 GLY A 13 ILE A 14 GLY A 15 LYS A 16 SITE 2 AC1 25 SER A 17 ALA A 18 ASN A 116 LYS A 117 SITE 3 AC1 25 ASP A 119 LEU A 120 SER A 145 ALA A 146 SITE 4 AC1 25 LYS A 147 HOH A 305 HOH A 307 HOH A 337 SITE 5 AC1 25 HOH A 338 HOH A 352 HOH A 355 HOH A 398 SITE 6 AC1 25 HOH A 402 HOH A 407 HOH A 408 HOH A 411 SITE 7 AC1 25 HOH A 418 CRYST1 77.751 77.751 55.935 90.00 90.00 120.00 P 3 2 1 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 0.012862 0.007426 0.000000 0.00000 SCALE2 0.000000 0.014851 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017878 0.00000