HEADER HYDROLASE 06-SEP-22 8EDY TITLE KRAS4B A146T 1-185 BOUND TO GDP 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 EC: 3.6.5.2; COMPND 6 ENGINEERED: YES; COMPND 7 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: KRAS, KRAS2, RASK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SMALL GTPASE, MUTANT KRAS, ONCOPROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.BETTS,K.L.ROSSMAN REVDAT 1 20-SEP-23 8EDY 0 JRNL AUTH L.BETTS,K.L.ROSSMAN JRNL TITL KRAS4B A146T 1-185 BOUND TO GDP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 122256 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.130 REMARK 3 FREE R VALUE TEST SET COUNT : 3832 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 39.1500 - 3.5500 1.00 4463 150 0.1514 0.1538 REMARK 3 2 3.5500 - 2.8200 0.99 4447 141 0.1472 0.1588 REMARK 3 3 2.8200 - 2.4600 0.99 4445 142 0.1541 0.1377 REMARK 3 4 2.4600 - 2.2400 0.99 4401 146 0.1436 0.1794 REMARK 3 5 2.2400 - 2.0800 0.99 4464 141 0.1411 0.1416 REMARK 3 6 2.0800 - 1.9600 0.99 4409 137 0.1455 0.1412 REMARK 3 7 1.9600 - 1.8600 0.99 4454 142 0.1555 0.1704 REMARK 3 8 1.8600 - 1.7800 0.99 4429 140 0.1557 0.1637 REMARK 3 9 1.7800 - 1.7100 1.00 4490 150 0.1625 0.1710 REMARK 3 10 1.7100 - 1.6500 1.00 4442 144 0.1578 0.2242 REMARK 3 11 1.6500 - 1.6000 1.00 4424 142 0.1583 0.1790 REMARK 3 12 1.6000 - 1.5500 1.00 4449 143 0.1634 0.1534 REMARK 3 13 1.5500 - 1.5100 1.00 4457 148 0.1675 0.1986 REMARK 3 14 1.5100 - 1.4700 0.99 4484 145 0.1828 0.2303 REMARK 3 15 1.4700 - 1.4400 0.99 4422 146 0.1814 0.2256 REMARK 3 16 1.4400 - 1.4100 0.99 4438 140 0.1812 0.1820 REMARK 3 17 1.4100 - 1.3800 0.99 4434 142 0.1809 0.1890 REMARK 3 18 1.3800 - 1.3600 0.99 4435 144 0.1812 0.1805 REMARK 3 19 1.3600 - 1.3300 0.99 4401 142 0.1824 0.1982 REMARK 3 20 1.3300 - 1.3100 0.99 4451 149 0.1837 0.1761 REMARK 3 21 1.3100 - 1.2900 0.99 4413 143 0.1901 0.2030 REMARK 3 22 1.2900 - 1.2700 0.99 4398 144 0.1995 0.2197 REMARK 3 23 1.2700 - 1.2500 0.99 4395 144 0.1945 0.1767 REMARK 3 24 1.2500 - 1.2300 0.99 4410 146 0.2188 0.2142 REMARK 3 25 1.2300 - 1.2200 0.99 4477 143 0.2331 0.2484 REMARK 3 26 1.2200 - 1.2000 0.97 4293 137 0.2867 0.3254 REMARK 3 27 1.2000 - 1.1800 0.72 3199 101 0.2857 0.2255 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) : 0.116 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.495 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.08 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 : 0.008 1527 REMARK 3 ANGLE : 1.134 2084 REMARK 3 CHIRALITY : 0.079 227 REMARK 3 PLANARITY : 0.008 272 REMARK 3 DIHEDRAL : 17.068 590 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 8EDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1000268281. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9782 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 122556 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.180 REMARK 200 RESOLUTION RANGE LOW (A) : 67.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.980 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4OBE REMARK 200 REMARK 200 REMARK: HEXAGONAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG3350, 200 MM LITHIUM CITRATE, REMARK 280 10 UM GDP, 1 MM MAGNESIUM CHLORIDE, 2 MM DTT, 20 MM SODIUM REMARK 280 CHLORIDE, 10 MM TRIS-HCL, PH 8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K 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 489 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 500 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 503 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 507 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 516 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 1 REMARK 465 LYS A 172 REMARK 465 ASP A 173 REMARK 465 GLY A 174 REMARK 465 LYS A 175 REMARK 465 LYS A 176 REMARK 465 LYS A 177 REMARK 465 LYS A 178 REMARK 465 LYS A 179 REMARK 465 LYS A 180 REMARK 465 SER A 181 REMARK 465 LYS A 182 REMARK 465 THR A 183 REMARK 465 LYS A 184 REMARK 465 SER A 185 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 -7.30 71.17 REMARK 500 SER A 122 58.36 -95.35 REMARK 500 ARG A 149 -0.35 78.12 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 516 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A 517 DISTANCE = 7.27 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8ED2 RELATED DB: PDB REMARK 900 8ED2 CONTAINS THE SAME PROTEIN BOUND TO GNP AND MG2+ REMARK 900 RELATED ID: 8EER RELATED DB: PDB REMARK 900 8EER CONTAINS THE SAME PROTEIN WITH A A146V MUTATION BOUND TO GDP REMARK 900 RELATED ID: 8ECR RELATED DB: PDB REMARK 900 8ECR CONTAINS THE WILD-TYPE FORM OF THE PROTEIN BOUND TO GDP AND REMARK 900 MG2+ DBREF 8EDY A 1 185 UNP P01116 RASK_HUMAN 1 185 SEQADV 8EDY THR A 146 UNP P01116 ALA 146 ENGINEERED MUTATION SEQADV 8EDY SER A 185 UNP P01116 CYS 185 CONFLICT SEQRES 1 A 185 MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY GLY SEQRES 2 A 185 VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN ASN SEQRES 3 A 185 HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SER SEQRES 4 A 185 TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS LEU SEQRES 5 A 185 LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SER SEQRES 6 A 185 ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY PHE SEQRES 7 A 185 LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE GLU SEQRES 8 A 185 ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL LYS SEQRES 9 A 185 ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN LYS SEQRES 10 A 185 CYS ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN ALA SEQRES 11 A 185 GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE GLU SEQRES 12 A 185 THR SER THR LYS THR ARG GLN GLY VAL ASP ASP ALA PHE SEQRES 13 A 185 TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU LYS SEQRES 14 A 185 MET SER LYS ASP GLY LYS LYS LYS LYS LYS LYS SER LYS SEQRES 15 A 185 THR LYS SER HET GDP A 201 38 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 HOH *217(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 SER A 171 1 21 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 GLY A 10 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 CRYST1 78.302 78.302 55.848 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 0.012771 0.007373 0.000000 0.00000 SCALE2 0.000000 0.014747 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017906 0.00000