HEADER CELL INVASION 09-SEP-19 6KX3 TITLE CRYSTAL STRUCTURE OF RHOA PROTEIN WITH COVALENT INHIBITOR DC-RHOIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSFORMING PROTEIN RHOA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RHOA PROTEIN, 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, COVALENT, COMPLEX, CELL INVASION EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,C.LUO REVDAT 2 22-NOV-23 6KX3 1 REMARK REVDAT 1 19-AUG-20 6KX3 0 JRNL AUTH Z.SUN,H.ZHANG,Y.ZHANG,L.LIAO,W.ZHOU,F.ZHANG,F.LIAN,J.HUANG, JRNL AUTH 2 P.XU,R.ZHANG,W.LU,M.ZHU,H.TAO,F.YANG,H.DING,S.CHEN,L.YUE, JRNL AUTH 3 B.ZHOU,N.ZHANG,M.TAN,H.JIANG,K.CHEN,B.LIU,C.LIU,Y.DANG,C.LUO JRNL TITL COVALENT INHIBITORS ALLOSTERICALLY BLOCK THE ACTIVATION OF JRNL TITL 2 RHO FAMILY PROTEINS AND SUPPRESS CANCER CELL INVASION. JRNL REF ADV SCI V. 7 00098 2020 JRNL REFN ESSN 2198-3844 JRNL PMID 32714746 JRNL DOI 10.1002/ADVS.202000098 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17114 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 838 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 45.8920 - 3.5995 1.00 2875 143 0.1928 0.2355 REMARK 3 2 3.5995 - 2.8571 1.00 2731 141 0.2295 0.2684 REMARK 3 3 2.8571 - 2.4960 1.00 2681 144 0.2467 0.3014 REMARK 3 4 2.4960 - 2.2678 1.00 2677 141 0.2487 0.3132 REMARK 3 5 2.2678 - 2.1053 1.00 2660 130 0.2501 0.3107 REMARK 3 6 2.1053 - 1.9811 1.00 2652 139 0.2566 0.2946 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.24 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 : 0.008 1424 REMARK 3 ANGLE : 1.036 1932 REMARK 3 CHIRALITY : 0.068 214 REMARK 3 PLANARITY : 0.006 245 REMARK 3 DIHEDRAL : 18.359 851 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 6KX3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013798. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17117 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.981 REMARK 200 RESOLUTION RANGE LOW (A) : 45.892 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 28.60 REMARK 200 R MERGE (I) : 0.07104 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 46.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.67190 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: PHASER REMARK 200 STARTING MODEL: 1FTN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML MUTANT, 0.2M NACL, 0.1M REMARK 280 ACETATE NA (PH 4.5), 1.26M AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 27.90650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.89200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.89200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.85975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.89200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.89200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.95325 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.89200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.89200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.85975 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.89200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.89200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.95325 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 27.90650 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 TOTAL BURIED SURFACE AREA: 600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 67 REMARK 465 ARG A 68 REMARK 465 LEU A 69 REMARK 465 ARG A 70 REMARK 465 PRO A 71 REMARK 465 LEU A 72 REMARK 465 SER A 73 REMARK 465 TYR A 74 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 97 O HOH A 301 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 49 -115.50 53.49 REMARK 500 LYS A 98 -56.84 -126.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8ZO A 202 DBREF 6KX3 A 1 181 UNP P61586 RHOA_HUMAN 1 181 SEQADV 6KX3 VAL A 16 UNP P61586 CYS 16 ENGINEERED MUTATION SEQADV 6KX3 SER A 20 UNP P61586 CYS 20 ENGINEERED MUTATION SEQADV 6KX3 VAL A 83 UNP P61586 CYS 83 ENGINEERED MUTATION SEQADV 6KX3 THR A 159 UNP P61586 CYS 159 ENGINEERED MUTATION SEQRES 1 A 181 MET ALA ALA ILE ARG LYS LYS LEU VAL ILE VAL GLY ASP SEQRES 2 A 181 GLY ALA VAL GLY LYS THR SER LEU LEU ILE VAL PHE SER SEQRES 3 A 181 LYS ASP GLN PHE PRO GLU VAL TYR VAL PRO THR VAL PHE SEQRES 4 A 181 GLU ASN TYR VAL ALA ASP ILE GLU VAL ASP GLY LYS GLN SEQRES 5 A 181 VAL GLU LEU ALA LEU TRP ASP THR ALA GLY GLN GLU ASP SEQRES 6 A 181 TYR ASP ARG LEU ARG PRO LEU SER TYR PRO ASP THR ASP SEQRES 7 A 181 VAL ILE LEU MET VAL PHE SER ILE ASP SER PRO ASP SER SEQRES 8 A 181 LEU GLU ASN ILE PRO GLU LYS TRP THR PRO GLU VAL LYS SEQRES 9 A 181 HIS PHE CYS PRO ASN VAL PRO ILE ILE LEU VAL GLY ASN SEQRES 10 A 181 LYS LYS ASP LEU ARG ASN ASP GLU HIS THR ARG ARG GLU SEQRES 11 A 181 LEU ALA LYS MET LYS GLN GLU PRO VAL LYS PRO GLU GLU SEQRES 12 A 181 GLY ARG ASP MET ALA ASN ARG ILE GLY ALA PHE GLY TYR SEQRES 13 A 181 MET GLU THR SER ALA LYS THR LYS ASP GLY VAL ARG GLU SEQRES 14 A 181 VAL PHE GLU MET ALA THR ARG ALA ALA LEU GLN ALA HET GDP A 201 28 HET 8ZO A 202 17 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM 8ZO PROP-2-ENYL (3R)-1,1-BIS(OXIDANYLIDENE)-2,3-DIHYDRO-1- HETNAM 2 8ZO BENZOTHIOPHENE-3-CARBOXYLATE FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 8ZO C12 H12 O4 S FORMUL 4 HOH *82(H2 O) HELIX 1 AA1 GLY A 17 ASP A 28 1 12 HELIX 2 AA2 SER A 88 LYS A 98 1 11 HELIX 3 AA3 LYS A 98 CYS A 107 1 10 HELIX 4 AA4 LYS A 118 ARG A 122 5 5 HELIX 5 AA5 ASP A 124 LYS A 133 1 10 HELIX 6 AA6 LYS A 140 GLY A 152 1 13 HELIX 7 AA7 GLY A 166 ALA A 181 1 16 SHEET 1 AA1 6 GLU A 40 VAL A 48 0 SHEET 2 AA1 6 LYS A 51 ASP A 59 -1 O VAL A 53 N ILE A 46 SHEET 3 AA1 6 ARG A 5 GLY A 12 1 N LYS A 6 O ALA A 56 SHEET 4 AA1 6 VAL A 79 SER A 85 1 O VAL A 83 N VAL A 11 SHEET 5 AA1 6 ILE A 112 ASN A 117 1 O ILE A 113 N ILE A 80 SHEET 6 AA1 6 GLY A 155 GLU A 158 1 O MET A 157 N GLY A 116 LINK SG CYS A 107 C8 8ZO A 202 1555 1555 1.68 CISPEP 1 PHE A 30 PRO A 31 0 -0.65 SITE 1 AC1 16 ALA A 15 VAL A 16 GLY A 17 LYS A 18 SITE 2 AC1 16 THR A 19 SER A 20 ASN A 117 LYS A 118 SITE 3 AC1 16 ASP A 120 LEU A 121 SER A 160 ALA A 161 SITE 4 AC1 16 LYS A 162 HOH A 315 HOH A 325 HOH A 331 SITE 1 AC2 7 LYS A 7 THR A 77 ILE A 80 GLU A 102 SITE 2 AC2 7 VAL A 103 PHE A 106 CYS A 107 CRYST1 91.784 91.784 55.813 90.00 90.00 90.00 P 43 21 2 8 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 0.010895 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010895 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017917 0.00000