HEADER SIGNALING PROTEIN, HYDROLASE 05-JAN-23 8FPX TITLE CRYSTAL STRUCTURE OF TUMOR RELATED RHOA MUTANT A161P IN COMPLEX WITH TITLE 2 GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSFORMING PROTEIN RHOA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RHO CDNA CLONE 12,H12; 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: RHOA, ARH12, ARHA, RHO12; SOURCE 6 EXPRESSION_SYSTEM: BACTERIA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 2; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T KEYWDS SMALL G PROTEINS, GTPASE, FAST-CYCLING MUTANT, A161P, SIGNALING KEYWDS 2 PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIN,Y.ZHENG REVDAT 2 04-SEP-24 8FPX 1 JRNL REVDAT 1 05-JUN-24 8FPX 0 JRNL AUTH Y.LIN,T.A.RAMELOT,S.SENYUZ,A.GURSOY,H.JANG,R.NUSSINOV, JRNL AUTH 2 O.KESKIN,Y.ZHENG JRNL TITL TUMOR-DERIVED RHOA MUTANTS INTERACT WITH EFFECTORS IN THE JRNL TITL 2 GDP-BOUND STATE. JRNL REF NAT COMMUN V. 15 7176 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39169042 JRNL DOI 10.1038/S41467-024-51445-Z REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 31397 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.350 REMARK 3 FREE R VALUE TEST SET COUNT : 1993 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 31.5700 - 3.5400 0.98 2127 138 0.1689 0.1982 REMARK 3 2 3.5400 - 2.8100 1.00 2131 145 0.1714 0.1910 REMARK 3 3 2.8100 - 2.4600 1.00 2104 152 0.1920 0.2410 REMARK 3 4 2.4600 - 2.2300 1.00 2147 145 0.1801 0.2360 REMARK 3 5 2.2300 - 2.0700 1.00 2128 148 0.1758 0.2020 REMARK 3 6 2.0700 - 1.9500 1.00 2112 150 0.1726 0.2076 REMARK 3 7 1.9500 - 1.8500 1.00 2130 131 0.1801 0.2328 REMARK 3 8 1.8500 - 1.7700 1.00 2112 147 0.2101 0.1981 REMARK 3 9 1.7700 - 1.7000 1.00 2086 144 0.1958 0.2347 REMARK 3 10 1.7000 - 1.6400 1.00 2153 145 0.2205 0.2575 REMARK 3 11 1.6400 - 1.5900 1.00 2119 142 0.2398 0.2372 REMARK 3 12 1.5900 - 1.5500 1.00 2099 143 0.2615 0.3336 REMARK 3 13 1.5500 - 1.5100 0.97 2086 138 0.3067 0.3387 REMARK 3 14 1.5100 - 1.4700 0.89 1870 125 0.3317 0.3735 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 1540 REMARK 3 ANGLE : 0.930 2101 REMARK 3 CHIRALITY : 0.088 228 REMARK 3 PLANARITY : 0.007 276 REMARK 3 DIHEDRAL : 16.381 608 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 3.7551 3.0414 2.1150 REMARK 3 T TENSOR REMARK 3 T11: 0.0824 T22: 0.1088 REMARK 3 T33: 0.0875 T12: -0.0073 REMARK 3 T13: 0.0530 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.5708 L22: 2.2842 REMARK 3 L33: 1.1972 L12: 0.1704 REMARK 3 L13: 0.0352 L23: -0.7519 REMARK 3 S TENSOR REMARK 3 S11: -0.0060 S12: 0.0031 S13: 0.0182 REMARK 3 S21: 0.0549 S22: -0.0603 S23: -0.0133 REMARK 3 S31: -0.0401 S32: -0.0159 S33: 0.0475 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 8FPX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271086. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31430 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 31.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: 1FTN REMARK 200 REMARK 200 REMARK: PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-24% PEG8K, 15% DIOXANE, 0.1M TRIS REMARK 280 PH8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 43.63250 REMARK 290 SMTRY3 2 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 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 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 LYS A 98 -54.55 -125.02 REMARK 500 LYS A 164 -5.82 80.54 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 497 DISTANCE = 6.84 ANGSTROMS 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 THR A 19 OG1 REMARK 620 2 PRO A 36 O 91.7 REMARK 620 3 GDP A 201 O3B 92.8 173.9 REMARK 620 4 HOH A 320 O 173.9 86.6 89.3 REMARK 620 5 HOH A 336 O 93.0 86.9 88.8 92.7 REMARK 620 6 HOH A 337 O 84.3 93.0 91.5 90.0 177.3 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8FPW RELATED DB: PDB REMARK 900 8FPW IS ANOTHER MUTANT OF THE SAME PROTEIN DBREF 8FPX A 1 181 UNP P61586 RHOA_HUMAN 1 181 SEQADV 8FPX GLY A -1 UNP P61586 EXPRESSION TAG SEQADV 8FPX SER A 0 UNP P61586 EXPRESSION TAG SEQADV 8FPX ASN A 25 UNP P61586 PHE 25 ENGINEERED MUTATION SEQADV 8FPX PRO A 161 UNP P61586 ALA 161 ENGINEERED MUTATION SEQRES 1 A 183 GLY SER MET ALA ALA ILE ARG LYS LYS LEU VAL ILE VAL SEQRES 2 A 183 GLY ASP GLY ALA CYS GLY LYS THR CYS LEU LEU ILE VAL SEQRES 3 A 183 ASN SER LYS ASP GLN PHE PRO GLU VAL TYR VAL PRO THR SEQRES 4 A 183 VAL PHE GLU ASN TYR VAL ALA ASP ILE GLU VAL ASP GLY SEQRES 5 A 183 LYS GLN VAL GLU LEU ALA LEU TRP ASP THR ALA GLY GLN SEQRES 6 A 183 GLU ASP TYR ASP ARG LEU ARG PRO LEU SER TYR PRO ASP SEQRES 7 A 183 THR ASP VAL ILE LEU MET CYS PHE SER ILE ASP SER PRO SEQRES 8 A 183 ASP SER LEU GLU ASN ILE PRO GLU LYS TRP THR PRO GLU SEQRES 9 A 183 VAL LYS HIS PHE CYS PRO ASN VAL PRO ILE ILE LEU VAL SEQRES 10 A 183 GLY ASN LYS LYS ASP LEU ARG ASN ASP GLU HIS THR ARG SEQRES 11 A 183 ARG GLU LEU ALA LYS MET LYS GLN GLU PRO VAL LYS PRO SEQRES 12 A 183 GLU GLU GLY ARG ASP MET ALA ASN ARG ILE GLY ALA PHE SEQRES 13 A 183 GLY TYR MET GLU CYS SER PRO LYS THR LYS ASP GLY VAL SEQRES 14 A 183 ARG GLU VAL PHE GLU MET ALA THR ARG ALA ALA LEU GLN SEQRES 15 A 183 ALA HET GDP A 201 28 HET MG A 202 1 HET DIO A 203 6 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM DIO 1,4-DIETHYLENE DIOXIDE FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 DIO C4 H8 O2 FORMUL 5 HOH *197(H2 O) HELIX 1 AA1 GLY A 17 LYS A 27 1 11 HELIX 2 AA2 GLN A 63 ASP A 67 5 5 HELIX 3 AA3 LEU A 69 TYR A 74 5 6 HELIX 4 AA4 SER A 88 LYS A 98 1 11 HELIX 5 AA5 LYS A 98 CYS A 107 1 10 HELIX 6 AA6 LYS A 118 ASN A 123 5 6 HELIX 7 AA7 ASP A 124 LYS A 133 1 10 HELIX 8 AA8 LYS A 140 GLY A 152 1 13 HELIX 9 AA9 GLY A 166 GLN A 180 1 15 SHEET 1 AA1 6 TYR A 42 GLU A 47 0 SHEET 2 AA1 6 GLN A 52 TRP A 58 -1 O VAL A 53 N ILE A 46 SHEET 3 AA1 6 ILE A 4 GLY A 12 1 N ILE A 4 O GLU A 54 SHEET 4 AA1 6 VAL A 79 SER A 85 1 O CYS A 83 N VAL A 11 SHEET 5 AA1 6 ILE A 112 ASN A 117 1 O ASN A 117 N PHE A 84 SHEET 6 AA1 6 GLY A 155 GLU A 158 1 O MET A 157 N GLY A 116 LINK OG1 THR A 19 MG MG A 202 1555 1555 2.07 LINK O PRO A 36 MG MG A 202 1555 1555 2.06 LINK O3B GDP A 201 MG MG A 202 1555 1555 2.06 LINK MG MG A 202 O HOH A 320 1555 1555 2.14 LINK MG MG A 202 O HOH A 336 1555 1555 2.08 LINK MG MG A 202 O HOH A 337 1555 1555 2.11 CRYST1 32.212 87.265 34.044 90.00 95.91 90.00 P 1 21 1 2 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 0.031044 0.000000 0.003211 0.00000 SCALE2 0.000000 0.011459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029531 0.00000