HEADER GTP-BINDING 15-DEC-96 1JAH TITLE H-RAS P21 PROTEIN MUTANT G12P, COMPLEXED WITH GUANOSINE-5'-[BETA, TITLE 2 GAMMA-METHYLENE] TRIPHOSPHATE AND MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-HA-RAS; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 1 - 166; COMPND 5 SYNONYM: G-DOMAIN; 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: H-RAS-1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: CK 600 K; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PTAC RAS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTAC KEYWDS GTP HYDROLYSIS, SIGNAL TRANSDUCTION, CANCER, G-DOMAIN, GTP-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR T.SCHWEINS,K.SCHEFFZEK,R.ASSHEUER,A.WITTINGHOFER REVDAT 5 03-APR-24 1JAH 1 REMARK REVDAT 4 07-FEB-24 1JAH 1 REMARK REVDAT 3 03-NOV-21 1JAH 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1JAH 1 VERSN REVDAT 1 23-JUL-97 1JAH 0 JRNL AUTH T.SCHWEINS,K.SCHEFFZEK,R.ASSHEUER,A.WITTINGHOFER JRNL TITL THE ROLE OF THE METAL ION IN THE P21RAS CATALYSED JRNL TITL 2 GTP-HYDROLYSIS: MN2+ VERSUS MG2+. JRNL REF J.MOL.BIOL. V. 266 847 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9102473 JRNL DOI 10.1006/JMBI.1996.0814 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.F.PAI,U.KRENGEL,G.A.PETSKO,R.S.GOODY,W.KABSCH, REMARK 1 AUTH 2 A.WITTINGHOFER REMARK 1 TITL REFINED CRYSTAL STRUCTURE OF THE TRIPHOSPHATE CONFORMATION REMARK 1 TITL 2 OF H-RAS P21 AT 1.35 A RESOLUTION: IMPLICATIONS FOR THE REMARK 1 TITL 3 MECHANISM OF GTP HYDROLYSIS REMARK 1 REF EMBO J. V. 9 2351 1990 REMARK 1 REFN ISSN 0261-4189 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.H.SEEBURG,W.W.COLBY,D.J.CAPON,D.V.GOEDDEL,A.D.LEVINSON REMARK 1 TITL BIOLOGICAL PROPERTIES OF HUMAN C-HA-RAS1 GENES MUTATED AT REMARK 1 TITL 2 CODON 12 REMARK 1 REF NATURE V. 312 71 1984 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13578 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1325 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 25 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.30 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.25 REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JAH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174298. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-DEC-91 REMARK 200 TEMPERATURE (KELVIN) : 277 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 : ELLIOTT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : FRANKS DOUBLE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS (W.KABSCH) REMARK 200 DATA SCALING SOFTWARE : XSCALE (KABSCH) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14178 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: C-H-RAS:GPPNP:MG2+ REMARK 200 REMARK 200 REMARK: CRYSTALS ARE ISOMORPHOUS TO C-H-RAS:GPPNP:MG2+, NO REMARK 200 ROTATION/TRANSLATION CALCULATIONS REQUIRED. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 107.09333 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 53.54667 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 53.54667 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 107.09333 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: DIMERIC 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 ASP A 33 76.11 -161.30 REMARK 500 ILE A 36 -60.03 -97.85 REMARK 500 LYS A 117 32.88 72.59 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 168 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 THR A 35 OG1 78.1 REMARK 620 3 GCP A 167 O2G 164.5 91.3 REMARK 620 4 GCP A 167 O2B 96.7 170.4 92.1 REMARK 620 5 HOH A 170 O 83.2 84.0 84.6 87.4 REMARK 620 6 HOH A 176 O 84.8 90.3 106.7 97.3 167.5 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 168 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GCP A 167 DBREF 1JAH A 1 166 UNP P01112 RASH_HUMAN 1 166 SEQADV 1JAH PRO A 12 UNP P01112 GLY 12 ENGINEERED MUTATION SEQADV 1JAH GLY A 122 UNP P01112 ALA 122 CONFLICT SEQRES 1 A 166 MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA PRO GLY 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 THR LYS SER PHE GLU SEQRES 8 A 166 ASP ILE HIS GLN 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 ALA GLY ARG THR VAL GLU SER ARG GLN ALA SEQRES 11 A 166 GLN ASP LEU ALA ARG SER TYR GLY ILE PRO TYR 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 HIS HET MG A 168 1 HET GCP A 167 32 HETNAM MG MAGNESIUM ION HETNAM GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER FORMUL 2 MG MG 2+ FORMUL 3 GCP C11 H18 N5 O13 P3 FORMUL 4 HOH *25(H2 O) HELIX 1 1 LYS A 16 GLN A 25 1 10 HELIX 2 2 GLU A 62 THR A 74 5 13 HELIX 3 3 THR A 87 LYS A 104 1 18 HELIX 4 4 SER A 127 TYR A 137 1 11 HELIX 5 5 VAL A 152 ARG A 164 1 13 SHEET 1 A 6 PRO A 140 GLU A 143 0 SHEET 2 A 6 PRO A 110 ASN A 116 1 N LEU A 113 O PRO A 140 SHEET 3 A 6 GLY A 77 ALA A 83 1 N PHE A 78 O PRO A 110 SHEET 4 A 6 THR A 2 GLY A 10 1 N VAL A 7 O GLY A 77 SHEET 5 A 6 GLU A 49 THR A 58 1 N LEU A 52 O THR A 2 SHEET 6 A 6 GLU A 37 ILE A 46 -1 N ILE A 46 O GLU A 49 LINK OG SER A 17 MG MG A 168 1555 1555 2.34 LINK OG1 THR A 35 MG MG A 168 1555 1555 2.22 LINK O2G GCP A 167 MG MG A 168 1555 1555 2.20 LINK O2B GCP A 167 MG MG A 168 1555 1555 2.18 LINK MG MG A 168 O HOH A 170 1555 1555 2.32 LINK MG MG A 168 O HOH A 176 1555 1555 2.31 SITE 1 AC1 5 SER A 17 THR A 35 GCP A 167 HOH A 170 SITE 2 AC1 5 HOH A 176 SITE 1 AC2 24 PRO A 12 GLY A 13 VAL A 14 GLY A 15 SITE 2 AC2 24 LYS A 16 SER A 17 ALA A 18 PHE A 28 SITE 3 AC2 24 VAL A 29 ASP A 30 TYR A 32 PRO A 34 SITE 4 AC2 24 THR A 35 ASN A 116 LYS A 117 ASP A 119 SITE 5 AC2 24 SER A 145 ALA A 146 LYS A 147 MG A 168 SITE 6 AC2 24 HOH A 169 HOH A 170 HOH A 175 HOH A 176 CRYST1 40.100 40.100 160.640 90.00 90.00 120.00 P 32 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 0.024938 0.014398 0.000000 0.00000 SCALE2 0.000000 0.028796 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006225 0.00000