HEADER SIGNALING PROTEIN 24-JUL-18 6E6H TITLE NRAS G13D BOUND TO GPPNHP (N13GNP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE NRAS; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-166; COMPND 5 SYNONYM: TRANSFORMING PROTEIN N-RAS; 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: NRAS, HRAS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS ONCOGENE, RAS, P21, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.W.JOHNSON,C.MATTOS REVDAT 4 13-MAR-24 6E6H 1 REMARK REVDAT 3 27-NOV-19 6E6H 1 REMARK REVDAT 2 04-SEP-19 6E6H 1 AUTHOR JRNL REMARK REVDAT 1 31-JUL-19 6E6H 0 JRNL AUTH C.W.JOHNSON,Y.J.LIN,D.REID,J.PARKER,S.PAVLOPOULOS, JRNL AUTH 2 P.DISCHINGER,C.GRAVEEL,A.J.AGUIRRE,M.STEENSMA,K.M.HAIGIS, JRNL AUTH 3 C.MATTOS JRNL TITL ISOFORM-SPECIFIC DESTABILIZATION OF THE ACTIVE SITE REVEALS JRNL TITL 2 A MOLECULAR MECHANISM OF INTRINSIC ACTIVATION OF KRAS G13D. JRNL REF CELL REP V. 28 1538 2019 JRNL REFN ESSN 2211-1247 JRNL PMID 31390567 JRNL DOI 10.1016/J.CELREP.2019.07.026 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 9745 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 976 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.57 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 6E6H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1000235544. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 173.15 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9752 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.56700 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9% 2-PROPANOL, 72 MM HEPES, 20% PEG REMARK 280 4000, 15% STABILIZATION BUFFER (20 MM HEPES, 50 MM NACL, 20 MM REMARK 280 MGCL2, AT PH 7.5), CRYSTALS WERE GROWN IN 1UL BY 1UL DROPS OF REMARK 280 MOTHER LIQUOR TO PROTEIN (12.2 MG/ML) NO CRYOPROTECTANT USED FOR REMARK 280 DIFFRACTION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 -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 29.77650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.78250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.77650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.78250 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ALA A 59 REMARK 465 GLY A 60 REMARK 465 GLN A 61 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 ARG A 68 REMARK 465 ASP A 69 REMARK 465 GLN A 70 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 LYS A 5 CD CE NZ REMARK 470 GLU A 31 CG CD OE1 OE2 REMARK 470 GLU A 49 CG CD OE1 OE2 REMARK 470 TYR A 71 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 LYS A 128 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 ARG A 149 -0.45 84.69 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 A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 GNP A 202 O1G 167.7 REMARK 620 3 GNP A 202 O1B 100.0 91.1 REMARK 620 4 HOH A 310 O 88.6 87.2 85.4 REMARK 620 5 HOH A 317 O 85.4 97.6 101.1 171.9 REMARK 620 6 HOH A 339 O 83.2 84.8 167.6 82.7 91.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6E6C RELATED DB: PDB REMARK 900 RELATED ID: 6E6P RELATED DB: PDB REMARK 900 RELATED ID: 6E6F RELATED DB: PDB REMARK 900 RELATED ID: 6E6G RELATED DB: PDB REMARK 900 RELATED ID: 6DZH RELATED DB: PDB DBREF 6E6H A 1 166 UNP P01111 RASN_HUMAN 1 166 SEQADV 6E6H ASP A 13 UNP P01111 GLY 13 ENGINEERED MUTATION SEQRES 1 A 166 MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY ASP SEQRES 2 A 166 VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN ASN SEQRES 3 A 166 HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SER SEQRES 4 A 166 TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS LEU SEQRES 5 A 166 LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SER SEQRES 6 A 166 ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY PHE SEQRES 7 A 166 LEU CYS VAL PHE ALA ILE ASN ASN SER LYS SER PHE ALA SEQRES 8 A 166 ASP ILE ASN LEU TYR ARG GLU GLN ILE LYS ARG VAL LYS SEQRES 9 A 166 ASP SER ASP ASP VAL PRO MET VAL LEU VAL GLY ASN LYS SEQRES 10 A 166 CYS ASP LEU PRO THR ARG THR VAL ASP THR LYS GLN ALA SEQRES 11 A 166 HIS GLU LEU ALA LYS SER TYR GLY ILE PRO PHE ILE GLU SEQRES 12 A 166 THR SER ALA LYS THR ARG GLN GLY VAL GLU ASP ALA PHE SEQRES 13 A 166 TYR THR LEU VAL ARG GLU ILE ARG GLN TYR HET MG A 201 1 HET GNP A 202 32 HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER FORMUL 2 MG MG 2+ FORMUL 3 GNP C10 H17 N6 O13 P3 FORMUL 4 HOH *80(H2 O) HELIX 1 AA1 GLY A 15 ASN A 26 1 12 HELIX 2 AA2 ASN A 86 ASP A 92 1 7 HELIX 3 AA3 ASP A 92 ASP A 105 1 14 HELIX 4 AA4 ASP A 126 GLY A 138 1 13 HELIX 5 AA5 GLY A 151 GLN A 165 1 15 SHEET 1 AA1 6 SER A 39 ILE A 46 0 SHEET 2 AA1 6 GLU A 49 ASP A 57 -1 O ILE A 55 N TYR A 40 SHEET 3 AA1 6 THR A 2 VAL A 9 1 N LEU A 6 O LEU A 56 SHEET 4 AA1 6 GLY A 77 ALA A 83 1 O LEU A 79 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 A 201 1555 1555 2.17 LINK MG MG A 201 O1G GNP A 202 1555 1555 1.93 LINK MG MG A 201 O1B GNP A 202 1555 1555 1.99 LINK MG MG A 201 O HOH A 310 1555 1555 2.27 LINK MG MG A 201 O HOH A 317 1555 1555 2.02 LINK MG MG A 201 O HOH A 339 1555 1555 2.08 SITE 1 AC1 5 SER A 17 GNP A 202 HOH A 310 HOH A 317 SITE 2 AC1 5 HOH A 339 SITE 1 AC2 28 GLY A 12 ASP A 13 VAL A 14 GLY A 15 SITE 2 AC2 28 LYS A 16 SER A 17 ALA A 18 PHE A 28 SITE 3 AC2 28 VAL A 29 ASP A 30 ASN A 116 LYS A 117 SITE 4 AC2 28 ASP A 119 LEU A 120 LYS A 135 SER A 145 SITE 5 AC2 28 ALA A 146 LYS A 147 MG A 201 HOH A 304 SITE 6 AC2 28 HOH A 305 HOH A 310 HOH A 316 HOH A 317 SITE 7 AC2 28 HOH A 336 HOH A 339 HOH A 356 HOH A 359 CRYST1 59.553 39.565 65.016 90.00 106.40 90.00 C 1 2 1 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 0.016792 0.000000 0.004942 0.00000 SCALE2 0.000000 0.025275 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016033 0.00000