HEADER GENE REGULATION/SIGNALING PROTEIN 27-DEC-99 1DPF TITLE CRYSTAL STRUCTURE OF A MG-FREE FORM OF RHOA COMPLEXED WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHOA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PRSET B KEYWDS PROTEIN RHOA-GDP COMPLEX, GENE REGULATION-SIGNALING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.SHIMIZU,K.IHARA,R.MAESAKI,S.KURODA,K.KAIBUCHI,T.HAKOSHIMA REVDAT 5 07-FEB-24 1DPF 1 REMARK SEQADV REVDAT 4 14-MAR-18 1DPF 1 SEQADV REVDAT 3 24-FEB-09 1DPF 1 VERSN REVDAT 2 01-APR-03 1DPF 1 JRNL REVDAT 1 21-JUN-00 1DPF 0 JRNL AUTH T.SHIMIZU,K.IHARA,R.MAESAKI,S.KURODA,K.KAIBUCHI,T.HAKOSHIMA JRNL TITL AN OPEN CONFORMATION OF SWITCH I REVEALED BY THE CRYSTAL JRNL TITL 2 STRUCTURE OF A MG2+-FREE FORM OF RHOA COMPLEXED WITH GDP. JRNL TITL 3 IMPLICATIONS FOR THE GDP/GTP EXCHANGE MECHANISM. JRNL REF J.BIOL.CHEM. V. 275 18311 2000 JRNL REFN ISSN 0021-9258 JRNL PMID 10748207 JRNL DOI 10.1074/JBC.M910274199 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 16088 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 SET) : 0.201 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 780 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 : 1399 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 187 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.290 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1DPF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1000010266. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-99 REMARK 200 TEMPERATURE (KELVIN) : 90.0 REMARK 200 PH : 5.5 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 : RIGAKU FR-C REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18926 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 49.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.33400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400, CITRATE, LITHIUM SULFATE, REMARK 280 MAGNESIUM CHLORIDE,, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 28.25000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.60000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.37500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.60000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.60000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.12500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.60000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.60000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 42.37500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.60000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.60000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 14.12500 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 28.25000 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 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 -53.68 -130.31 REMARK 500 PRO A 138 150.56 -49.47 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 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A2B RELATED DB: PDB REMARK 900 1A2B CONTAINS THE SAME PROTEIN COMPLEXED WITH GTPGS DBREF 1DPF A 1 180 UNP P61586 RHOA_HUMAN 1 180 SEQADV 1DPF VAL A 14 UNP P61586 GLY 14 ENGINEERED MUTATION SEQRES 1 A 180 MET ALA ALA ILE ARG LYS LYS LEU VAL ILE VAL GLY ASP SEQRES 2 A 180 VAL ALA CYS GLY LYS THR CYS LEU LEU ILE VAL PHE SER SEQRES 3 A 180 LYS ASP GLN PHE PRO ALA VAL TYR VAL PRO THR VAL PHE SEQRES 4 A 180 GLU ASN TYR VAL ALA ASP ILE GLU VAL ASP GLY LYS GLN SEQRES 5 A 180 VAL GLU LEU ALA LEU TRP ASP THR ALA GLY GLN GLU ASP SEQRES 6 A 180 TYR ASP ARG ALA ARG PRO LEU SER TYR PRO ASP THR ASP SEQRES 7 A 180 VAL ILE LEU MET CYS PHE SER ILE ASP SER PRO ASP SER SEQRES 8 A 180 LEU GLU ASN ILE PRO GLU LYS TRP THR PRO GLU VAL LYS SEQRES 9 A 180 HIS PHE CYS PRO ASN VAL PRO ILE ILE LEU VAL GLY ASN SEQRES 10 A 180 LYS LYS ASP LEU ARG ASN ASP GLU HIS THR ALA ARG GLU SEQRES 11 A 180 LEU ALA LYS MET LYS GLN GLU PRO VAL LYS PRO ALA GLU SEQRES 12 A 180 GLY ARG ASP MET ALA ASN ARG ILE GLY ALA PHE GLY TYR SEQRES 13 A 180 MET GLU CYS SER ALA LYS THR LYS ASP GLY VAL ARG GLU SEQRES 14 A 180 VAL PHE GLU MET ALA THR ARG ALA ALA LEU GLN HET GDP A 200 28 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 HOH *187(H2 O) HELIX 1 1 GLY A 17 ASP A 28 1 12 HELIX 2 2 ALA A 69 TYR A 74 5 6 HELIX 3 3 SER A 88 LYS A 98 1 11 HELIX 4 4 LYS A 98 CYS A 107 1 10 HELIX 5 5 LYS A 118 ARG A 122 5 5 HELIX 6 6 ASP A 124 LYS A 133 1 10 HELIX 7 7 LYS A 140 GLY A 152 1 13 HELIX 8 8 GLY A 166 GLN A 180 1 15 SHEET 1 A 6 GLU A 40 VAL A 48 0 SHEET 2 A 6 LYS A 51 ASP A 59 -1 N LYS A 51 O VAL A 48 SHEET 3 A 6 ILE A 4 VAL A 11 1 O ILE A 4 N GLU A 54 SHEET 4 A 6 VAL A 79 SER A 85 1 O VAL A 79 N VAL A 9 SHEET 5 A 6 ILE A 112 ASN A 117 1 N ILE A 113 O ILE A 80 SHEET 6 A 6 GLY A 155 GLU A 158 1 O GLY A 155 N LEU A 114 CISPEP 1 PHE A 30 PRO A 31 0 0.09 SITE 1 AC1 20 VAL A 14 ALA A 15 CYS A 16 GLY A 17 SITE 2 AC1 20 LYS A 18 THR A 19 CYS A 20 ALA A 61 SITE 3 AC1 20 LYS A 118 ASP A 120 LEU A 121 SER A 160 SITE 4 AC1 20 ALA A 161 LYS A 162 HOH A 308 HOH A 310 SITE 5 AC1 20 HOH A 337 HOH A 350 HOH A 440 HOH A 474 CRYST1 91.200 91.200 56.500 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 0.010965 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010965 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017699 0.00000