HEADER HYDROLASE 13-MAR-23 8GI3 TITLE CRYSTAL STRUCTURE OF RHOA MUTANT L69P COMPLEXED WITH 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: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SMALL GTPASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.CHEN,X.QIAN,M.CHANDRAVANSHI,D.R.LOWY,K.J.WALTERS REVDAT 2 03-APR-24 8GI3 1 TITLE REVDAT 1 20-MAR-24 8GI3 0 JRNL AUTH X.CHEN,X.QIAN,D.R.LOWY,K.J.WALTERS JRNL TITL RAS-LIKE GTPASES MUTANTS STRUCTURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC V5.5 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 26852 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1341 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1417 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 185 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.19000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.078 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.044 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.131 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8GI3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000272944. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26852 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 50.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.14300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP V11.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CITRATE DIBASIC (PH REMARK 280 5.1), 20% PEG3350, MICROBATCH, TEMPERATURE 293.2K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.02400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.25200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.04050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.25200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.02400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.04050 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 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 -2 REMARK 465 PRO A -1 REMARK 465 LEU A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ARG A 182 REMARK 465 ARG A 183 REMARK 465 GLY A 184 REMARK 465 LYS A 185 REMARK 465 LYS A 186 REMARK 465 LYS A 187 REMARK 465 SER A 188 REMARK 465 GLY A 189 REMARK 465 CYS A 190 REMARK 465 LEU A 191 REMARK 465 VAL A 192 REMARK 465 LEU A 193 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 -57.29 -133.11 REMARK 500 LYS A 164 -1.80 74.81 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 THR A 19 OG1 REMARK 620 2 PRO A 36 O 89.9 REMARK 620 3 GDP A 201 O1B 91.1 176.3 REMARK 620 4 HOH A 343 O 83.6 89.9 93.8 REMARK 620 5 HOH A 344 O 90.2 86.7 89.8 172.9 REMARK 620 6 HOH A 352 O 172.7 86.0 93.4 90.3 95.6 REMARK 620 N 1 2 3 4 5 DBREF 8GI3 A 1 193 UNP P61586 RHOA_HUMAN 1 193 SEQADV 8GI3 GLY A -2 UNP P61586 EXPRESSION TAG SEQADV 8GI3 PRO A -1 UNP P61586 EXPRESSION TAG SEQADV 8GI3 LEU A 0 UNP P61586 EXPRESSION TAG SEQADV 8GI3 PRO A 69 UNP P61586 LEU 69 ENGINEERED MUTATION SEQRES 1 A 196 GLY PRO LEU MET ALA ALA ILE ARG LYS LYS LEU VAL ILE SEQRES 2 A 196 VAL GLY ASP GLY ALA CYS GLY LYS THR CYS LEU LEU ILE SEQRES 3 A 196 VAL PHE SER LYS ASP GLN PHE PRO GLU VAL TYR VAL PRO SEQRES 4 A 196 THR VAL PHE GLU ASN TYR VAL ALA ASP ILE GLU VAL ASP SEQRES 5 A 196 GLY LYS GLN VAL GLU LEU ALA LEU TRP ASP THR ALA GLY SEQRES 6 A 196 GLN GLU ASP TYR ASP ARG PRO ARG PRO LEU SER TYR PRO SEQRES 7 A 196 ASP THR ASP VAL ILE LEU MET CYS PHE SER ILE ASP SER SEQRES 8 A 196 PRO ASP SER LEU GLU ASN ILE PRO GLU LYS TRP THR PRO SEQRES 9 A 196 GLU VAL LYS HIS PHE CYS PRO ASN VAL PRO ILE ILE LEU SEQRES 10 A 196 VAL GLY ASN LYS LYS ASP LEU ARG ASN ASP GLU HIS THR SEQRES 11 A 196 ARG ARG GLU LEU ALA LYS MET LYS GLN GLU PRO VAL LYS SEQRES 12 A 196 PRO GLU GLU GLY ARG ASP MET ALA ASN ARG ILE GLY ALA SEQRES 13 A 196 PHE GLY TYR MET GLU CYS SER ALA LYS THR LYS ASP GLY SEQRES 14 A 196 VAL ARG GLU VAL PHE GLU MET ALA THR ARG ALA ALA LEU SEQRES 15 A 196 GLN ALA ARG ARG GLY LYS LYS LYS SER GLY CYS LEU VAL SEQRES 16 A 196 LEU HET GDP A 201 28 HET MG A 202 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 HOH *185(H2 O) HELIX 1 AA1 GLY A 17 ASP A 28 1 12 HELIX 2 AA2 PRO A 69 TYR A 74 5 6 HELIX 3 AA3 SER A 88 LYS A 98 1 11 HELIX 4 AA4 LYS A 98 CYS A 107 1 10 HELIX 5 AA5 LYS A 118 ARG A 122 5 5 HELIX 6 AA6 ASP A 124 MET A 134 1 11 HELIX 7 AA7 LYS A 140 GLY A 152 1 13 HELIX 8 AA8 GLY A 166 GLN A 180 1 15 SHEET 1 AA1 6 TYR A 42 VAL A 48 0 SHEET 2 AA1 6 LYS A 51 TRP A 58 -1 O LEU A 55 N ALA A 44 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 GLY A 155 N LEU A 114 LINK OG1 THR A 19 MG MG A 202 1555 1555 2.15 LINK O PRO A 36 MG MG A 202 1555 1555 2.08 LINK O1B GDP A 201 MG MG A 202 1555 1555 2.03 LINK MG MG A 202 O HOH A 343 1555 1555 2.09 LINK MG MG A 202 O HOH A 344 1555 1555 2.07 LINK MG MG A 202 O HOH A 352 1555 1555 2.08 CRYST1 32.048 64.081 82.504 90.00 90.00 90.00 P 21 21 21 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 0.031203 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012121 0.00000