HEADER ONCOPROTEIN, HYDROLASE 14-SEP-22 8EIE TITLE KRAS4B K117N 1-185 BOUND TO GNP-MG2+ 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 8EIE 0 JRNL AUTH L.BETTS,K.L.ROSSMAN JRNL TITL A CRYSTALLOGRAPHIC VIEW OF THE FAST-CYCLING KRAS MUTANT, JRNL TITL 2 K117N JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.41 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.270 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 34082 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1985 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 39.4900 - 3.4000 1.00 2343 150 0.1672 0.1846 REMARK 3 2 3.3900 - 2.7000 1.00 2352 142 0.1649 0.1805 REMARK 3 3 2.7000 - 2.3600 1.00 2336 140 0.1747 0.2015 REMARK 3 4 2.3600 - 2.1400 1.00 2350 143 0.1739 0.2105 REMARK 3 5 2.1400 - 1.9900 1.00 2325 146 0.1855 0.2172 REMARK 3 6 1.9900 - 1.8700 0.99 2329 143 0.1908 0.2154 REMARK 3 7 1.8700 - 1.7800 0.99 2353 139 0.2015 0.2190 REMARK 3 8 1.7800 - 1.7000 0.99 2304 148 0.2081 0.2355 REMARK 3 9 1.7000 - 1.6300 0.98 2305 146 0.2184 0.2502 REMARK 3 10 1.6300 - 1.5800 0.98 2289 140 0.2102 0.2230 REMARK 3 11 1.5800 - 1.5300 0.97 2265 138 0.2102 0.2811 REMARK 3 12 1.5300 - 1.4800 0.95 2234 138 0.2195 0.2317 REMARK 3 13 1.4800 - 1.4500 0.94 2190 136 0.2298 0.2452 REMARK 3 14 1.4500 - 1.4100 0.91 2122 136 0.2457 0.2653 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) : 0.145 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.381 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.05 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 : 0.011 1412 REMARK 3 ANGLE : 1.200 1918 REMARK 3 CHIRALITY : 0.090 214 REMARK 3 PLANARITY : 0.011 245 REMARK 3 DIHEDRAL : 17.277 522 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 8EIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1000268515. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34844 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 200 RESOLUTION RANGE LOW (A) : 39.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : 0.60700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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: 6VC8 REMARK 200 REMARK 200 REMARK: SMALL CHUNKS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG4000, 0.2 M SODIUM ACETATE, 0.1 REMARK 280 M TRIS-HCL PH 8.5, 20 MM SODIUM CHLORIDE, 1 MM MAGNESIUM REMARK 280 CHLORIDE, 2 MM DTT, 2 MM GNP, 15 MG/ML KRAS K117N, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 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 1.000000 0.000000 0.000000 39.49000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.79956 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.90333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 39.49000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 22.79956 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.90333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 39.49000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 22.79956 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.90333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.59912 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 51.80667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 45.59912 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 51.80667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 45.59912 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 51.80667 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 A1204 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 GLU A 62 REMARK 465 GLU A 63 REMARK 465 TYR A 64 REMARK 465 SER A 65 REMARK 465 ALA A 66 REMARK 465 MET A 67 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 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 30 CG OD1 OD2 REMARK 470 GLU A 31 CG CD OE1 OE2 REMARK 470 GLN A 61 CG CD OE1 NE2 REMARK 470 LYS A 169 CG CD CE NZ REMARK 470 LYS A 172 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 GLU A 37 127.93 -170.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 THR A 35 OG1 85.4 REMARK 620 3 GNP A1001 O1G 173.6 88.2 REMARK 620 4 GNP A1001 O2B 91.4 176.3 95.0 REMARK 620 5 HOH A1117 O 90.4 90.6 89.1 87.5 REMARK 620 6 HOH A1119 O 87.6 91.1 93.0 90.7 177.3 REMARK 620 N 1 2 3 4 5 DBREF 8EIE A 1 185 UNP P01116 RASK_HUMAN 1 185 SEQADV 8EIE ASN A 117 UNP P01116 LYS 117 ENGINEERED MUTATION SEQADV 8EIE 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 ASN 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 ALA 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 GNP A1001 44 HET MG A1002 1 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION FORMUL 2 GNP C10 H17 N6 O13 P3 FORMUL 3 MG MG 2+ FORMUL 4 HOH *108(H2 O) HELIX 1 AA1 GLY A 15 ASN A 26 1 12 HELIX 2 AA2 ASP A 69 GLY A 75 1 7 HELIX 3 AA3 ASN A 86 LYS A 104 1 19 HELIX 4 AA4 ASP A 126 GLY A 138 1 13 HELIX 5 AA5 GLY A 151 LYS A 175 1 25 SHEET 1 AA1 6 GLU A 37 ILE A 46 0 SHEET 2 AA1 6 GLU A 49 THR A 58 -1 O ASP A 57 N ASP A 38 SHEET 3 AA1 6 THR A 2 VAL A 9 1 N VAL A 8 O LEU A 56 SHEET 4 AA1 6 GLY A 77 ALA A 83 1 O VAL A 81 N VAL A 9 SHEET 5 AA1 6 MET A 111 ASN A 116 1 O ASN A 116 N PHE A 82 SHEET 6 AA1 6 PHE A 141 GLU A 143 1 O ILE A 142 N LEU A 113 LINK OG SER A 17 MG MG A1002 1555 1555 2.04 LINK OG1 THR A 35 MG MG A1002 1555 1555 2.05 LINK O1G GNP A1001 MG MG A1002 1555 1555 2.00 LINK O2B GNP A1001 MG MG A1002 1555 1555 2.07 LINK MG MG A1002 O HOH A1117 1555 1555 2.12 LINK MG MG A1002 O HOH A1119 1555 1555 2.09 CRYST1 78.980 78.980 77.710 90.00 90.00 120.00 H 3 9 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 0.012661 0.007310 0.000000 0.00000 SCALE2 0.000000 0.014620 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012868 0.00000