HEADER ONCOPROTEIN 19-APR-23 8OSO TITLE GTPASE HRAS IN COMPLEX WITH ZN-CYCLEN UNDER 500 MPA PRESSURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE HRAS; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GTPASE HRAS N-TERMINALLY PROCESSED; COMPND 5 SYNONYM: H-RAS-1,HA-RAS,TRANSFORMING PROTEIN P21,C-H-RAS,P21RAS; COMPND 6 EC: 3.6.5.2; COMPND 7 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: HRAS, HRAS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: CK600K; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTAC KEYWDS G PROTEIN, SIGNALING PROTEIN, HPMX, ONCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.COLLOC'H,T.PRANGE,E.GIRARD,H.R.KALBITZER REVDAT 1 08-MAY-24 8OSO 0 JRNL AUTH E.GIRARD,P.LOPES,M.SPOERNER,A.C.DHAUSSY,T.PRANGE, JRNL AUTH 2 H.R.KALBITZER,N.COLLOC'H JRNL TITL HIGH PRESSURE PROMOTES BINDING OF THE ALLOSTERIC INHIBITOR JRNL TITL 2 ZN2+-CYCLEN IN CRYSTALS OF ACTIVATED H-RAS. JRNL REF CHEMISTRY 00304 2024 JRNL REFN ISSN 0947-6539 JRNL PMID 38647362 JRNL DOI 10.1002/CHEM.202400304 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.GIRARD,P.LOPES,M.SPOERNER,A.C.DHAUSSY,T.PRANGE, REMARK 1 AUTH 2 H.R.KALBITZER,N.COLLOC'H REMARK 1 TITL EQUILIBRIA BETWEEN CONFORMATIONAL STATES OF THE RAS ONCOGENE REMARK 1 TITL 2 PROTEIN REVEALED BY HIGH PRESSURE CRYSTALLOGRAPHY. REMARK 1 REF CHEM SCI V. 13 2001 2022 REMARK 1 REFN ISSN 2041-6520 REMARK 1 PMID 35308861 REMARK 1 DOI 10.1107/S0907444910007493 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 4945 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.850 REMARK 3 FREE R VALUE TEST SET COUNT : 487 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 32.7300 - 3.6100 0.93 1552 173 0.2060 0.2471 REMARK 3 2 3.6000 - 2.8600 0.95 1481 162 0.2379 0.2878 REMARK 3 3 2.8600 - 2.5000 0.93 1425 152 0.2919 0.3565 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.354 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.178 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.21 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 : 0.002 1406 REMARK 3 ANGLE : 0.476 1900 REMARK 3 CHIRALITY : 0.040 208 REMARK 3 PLANARITY : 0.004 242 REMARK 3 DIHEDRAL : 18.622 531 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 8OSO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-APR-23. REMARK 100 THE DEPOSITION ID IS D_1292129963. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : CRISTAL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.51035 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX SX-165MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 6.5.015 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4948 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 33.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.19600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.91800 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: MOLREP 11.4.03 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 MM TRIS HCL, 10 MM MGCL2, 2 MM DTE, REMARK 280 26-30 % PEG-400, PH 7.5, BATCH MODE, TEMPERATURE 293K 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 106.54267 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 53.27133 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 53.27133 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 106.54267 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 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 330 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 ASP A 30 -158.81 -121.03 REMARK 500 ASP A 38 -52.14 63.93 REMARK 500 MET A 72 -23.38 63.53 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 GNP A 201 O2G 131.0 REMARK 620 3 GNP A 201 O2B 88.0 85.8 REMARK 620 4 HOH A 301 O 72.5 60.7 66.0 REMARK 620 5 HOH A 302 O 70.6 80.9 135.9 70.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 205 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GNP A 201 O1G REMARK 620 2 YCN A 204 N1 105.0 REMARK 620 3 YCN A 204 N2 133.1 76.1 REMARK 620 4 YCN A 204 N3 121.6 132.0 80.0 REMARK 620 5 YCN A 204 N4 123.3 72.9 102.2 72.4 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8OSN RELATED DB: PDB REMARK 900 SAME COMPLEX AT AMBIENT PRESSURE REMARK 900 RELATED ID: 8OSM RELATED DB: PDB REMARK 900 SAME COMPLEX AT 200 MPA DBREF 8OSO A 1 166 UNP P01112 RASH_HUMAN 1 166 SEQRES 1 A 166 MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY 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 ALA 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 GNP A 201 32 HET MG A 202 1 HET PGE A 203 10 HET YCN A 204 12 HET ZN A 205 1 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM PGE TRIETHYLENE GLYCOL HETNAM YCN 1,4,7,10-TETRAAZACYCLODODECANE HETNAM ZN ZINC ION HETSYN YCN CYCLEN FORMUL 2 GNP C10 H17 N6 O13 P3 FORMUL 3 MG MG 2+ FORMUL 4 PGE C6 H14 O4 FORMUL 5 YCN C8 H20 N4 FORMUL 6 ZN ZN 2+ FORMUL 7 HOH *40(H2 O) HELIX 1 AA1 GLY A 15 GLN A 25 1 11 HELIX 2 AA2 GLN A 61 GLU A 63 5 3 HELIX 3 AA3 TYR A 64 TYR A 71 1 8 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 GLU A 126 GLY A 138 1 13 HELIX 7 AA7 GLY A 151 HIS A 166 1 16 SHEET 1 AA1 6 SER A 39 ILE A 46 0 SHEET 2 AA1 6 GLU A 49 ASP A 57 -1 O GLU A 49 N ILE A 46 SHEET 3 AA1 6 GLU A 3 GLY A 10 1 N LEU A 6 O ASP A 54 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 VAL A 112 N CYS A 80 SHEET 6 AA1 6 TYR A 141 GLU A 143 1 O ILE A 142 N GLY A 115 LINK OG SER A 17 MG MG A 202 1555 1555 2.24 LINK O2G GNP A 201 MG MG A 202 1555 1555 1.97 LINK O2B GNP A 201 MG MG A 202 1555 1555 2.23 LINK O1G GNP A 201 ZN ZN A 205 1555 1555 1.90 LINK MG MG A 202 O HOH A 301 1555 1555 2.53 LINK MG MG A 202 O HOH A 302 1555 1555 2.35 LINK N1 YCN A 204 ZN ZN A 205 1555 1555 2.25 LINK N2 YCN A 204 ZN ZN A 205 1555 1555 2.19 LINK N3 YCN A 204 ZN ZN A 205 1555 1555 2.04 LINK N4 YCN A 204 ZN ZN A 205 1555 1555 2.08 CRYST1 38.612 38.612 159.814 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 0.025899 0.014953 0.000000 0.00000 SCALE2 0.000000 0.029905 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006257 0.00000