PDB Short entry for 2BXW HEADER INHIBITOR 27-JUL-05 2BXW TITLE CRYSTAL STRUCTURE OF RHOGDI LYS(135,138,141)TYR MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHO GDP-DISSOCIATION INHIBITOR 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ISOPRENYL-BINDING DOMAIN, RESIDUES 67-204; COMPND 5 SYNONYM: RHO GDI 1, RHO-GDI ALPHA; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGST-PARALLEL1; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: RHOGDIY135, 138, 141Y KEYWDS INHIBITOR, CRYSTAL ENGINEERING, RATIONAL SURFACE MUTAGENESIS, GTPASE KEYWDS 2 ACTIVATION EXPDTA X-RAY DIFFRACTION AUTHOR M.SIKORSKA,D.R.COOPER,J.OTLEWSKI,Z.S.DEREWENDA REVDAT 5 13-DEC-23 2BXW 1 REMARK REVDAT 4 30-MAY-12 2BXW 1 AUTHOR REMARK HETSYN REVDAT 3 13-JUL-11 2BXW 1 VERSN REVDAT 2 24-FEB-09 2BXW 1 VERSN REVDAT 1 19-AUG-05 2BXW 0 JRNL AUTH D.R.COOPER,T.BOCZEK,K.GRELEWSKA,M.PINKOWSKA,M.SIKORSKA, JRNL AUTH 2 M.ZAWADZKI,Z.S.DEREWENDA JRNL TITL PROTEIN CRYSTALLIZATION BY SURFACE ENTROPY REDUCTION: JRNL TITL 2 OPTIMIZATION OF THE SER STRATEGY JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 63 636 2007 JRNL REFN ISSN 0907-4449 JRNL PMID 17452789 JRNL DOI 10.1107/S0907444907010931 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 22152 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1056 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1317 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2238 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 213 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.08000 REMARK 3 B22 (A**2) : 1.08000 REMARK 3 B33 (A**2) : -1.61000 REMARK 3 B12 (A**2) : 0.54000 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): 0.196 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.182 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.182 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2305 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2063 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3117 ; 2.264 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4795 ; 1.402 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 274 ; 6.061 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;30.392 ;23.462 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 400 ;13.872 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;19.956 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 335 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2514 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 486 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 305 ; 0.170 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1972 ; 0.152 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1052 ; 0.169 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1421 ; 0.078 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 172 ; 0.160 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 6 ; 0.110 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 35 ; 0.154 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.220 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1787 ; 0.753 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2230 ; 0.805 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1144 ; 1.263 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 887 ; 1.740 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 65 A 202 REMARK 3 ORIGIN FOR THE GROUP (A): 24.0300 17.5280 25.0310 REMARK 3 T TENSOR REMARK 3 T11: -0.1142 T22: -0.0975 REMARK 3 T33: 0.0636 T12: 0.0092 REMARK 3 T13: 0.0189 T23: -0.0074 REMARK 3 L TENSOR REMARK 3 L11: 0.2257 L22: 3.2444 REMARK 3 L33: 1.3476 L12: -0.6363 REMARK 3 L13: -0.1487 L23: 1.7254 REMARK 3 S TENSOR REMARK 3 S11: -0.0019 S12: -0.0333 S13: 0.0221 REMARK 3 S21: 0.0394 S22: -0.0957 S23: 0.0895 REMARK 3 S31: 0.0070 S32: -0.1034 S33: 0.0975 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 65 B 202 REMARK 3 ORIGIN FOR THE GROUP (A): 26.1540 -13.0690 0.8910 REMARK 3 T TENSOR REMARK 3 T11: -0.1292 T22: -0.1018 REMARK 3 T33: 0.0315 T12: -0.0131 REMARK 3 T13: 0.0153 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.3029 L22: 4.4177 REMARK 3 L33: 1.4503 L12: 0.2744 REMARK 3 L13: 0.2676 L23: 2.3089 REMARK 3 S TENSOR REMARK 3 S11: 0.0030 S12: 0.0075 S13: -0.0383 REMARK 3 S21: -0.0053 S22: -0.0705 S23: 0.0944 REMARK 3 S31: -0.0251 S32: -0.0750 S33: 0.0675 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2BXW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1290024875. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.88 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 : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23248 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.18000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.440 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1KMT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4M NA FORMATE, PH 7.88 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 57.21967 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 114.43933 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 114.43933 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 57.21967 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 135 TO TYR REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 138 TO TYR REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 141 TO TYR REMARK 400 ENGINEERED RESIDUE IN CHAIN B, LYS 135 TO TYR REMARK 400 ENGINEERED RESIDUE IN CHAIN B, LYS 138 TO TYR REMARK 400 ENGINEERED RESIDUE IN CHAIN B, LYS 141 TO TYR REMARK 400 REMARK 400 REGULATES THE GDP/GTP EXCHANGE REACTION OF THE RHO REMARK 400 PROTEINS BY INHIBITING THE DISSOCIATION OF GDP FROM THEM, REMARK 400 AND THE SUBSEQUENT BINDING OF GTP TO THEM. 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 64 REMARK 465 LYS A 203 REMARK 465 ASP A 204 REMARK 465 GLY B 64 REMARK 465 LYS B 203 REMARK 465 ASP B 204 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 O HOH B 2044 O HOH B 2071 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 111 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 120 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 120 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 172 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 180 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 111 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 111 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 134 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES 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 MET A 66 27.30 43.72 REMARK 500 ARG B 120 -65.13 73.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 65 MET A 66 -108.31 REMARK 500 MET A 66 VAL A 67 149.32 REMARK 500 ALA B 65 MET B 66 -117.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 1205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CC0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RHOA.GDP-RHOGDI COMPLEX REMARK 900 RELATED ID: 1FSO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TRUNCATED HUMAN RHOGDI QUADRUPLE MUTANT REMARK 900 RELATED ID: 1FST RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TRUNCATED HUMAN RHOGDI TRIPLE MUTANT REMARK 900 RELATED ID: 1FT0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TRUNCATED HUMAN RHOGDI K113A MUTANT REMARK 900 RELATED ID: 1FT3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TRUNCATED RHOGDI K141A MUTANT REMARK 900 RELATED ID: 1HH4 RELATED DB: PDB REMARK 900 RAC1-RHOGDI COMPLEX INVOLVED IN NADPH OXIDASE ACTIVATION REMARK 900 RELATED ID: 1KMT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RHOGDI GLU(154,155) ALA MUTANT REMARK 900 RELATED ID: 1QVY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RHOGDI K(199,200)R DOUBLE MUTANT REMARK 900 RELATED ID: 1RHO RELATED DB: PDB REMARK 900 STRUCTURE OF RHO GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 N-TERMINAL RESIDUES WERE CLONING ARTIFACTS. LYSINE REMARK 999 MUTATIONS TO PROMOTE CRYSTALLIZATION. DBREF 2BXW A 64 66 PDB 2BXW 2BXW 64 66 DBREF 2BXW A 67 204 UNP P52565 GDIR_HUMAN 67 204 DBREF 2BXW B 64 66 PDB 2BXW 2BXW 64 66 DBREF 2BXW B 67 204 UNP P52565 GDIR_HUMAN 67 204 SEQADV 2BXW TYR A 135 UNP P52565 LYS 135 ENGINEERED MUTATION SEQADV 2BXW TYR A 138 UNP P52565 LYS 138 ENGINEERED MUTATION SEQADV 2BXW TYR A 141 UNP P52565 LYS 141 ENGINEERED MUTATION SEQADV 2BXW TYR B 135 UNP P52565 LYS 135 ENGINEERED MUTATION SEQADV 2BXW TYR B 138 UNP P52565 LYS 138 ENGINEERED MUTATION SEQADV 2BXW TYR B 141 UNP P52565 LYS 141 ENGINEERED MUTATION SEQRES 1 A 141 GLY ALA MET VAL PRO ASN VAL VAL VAL THR GLY LEU THR SEQRES 2 A 141 LEU VAL CYS SER SER ALA PRO GLY PRO LEU GLU LEU ASP SEQRES 3 A 141 LEU THR GLY ASP LEU GLU SER PHE LYS LYS GLN SER PHE SEQRES 4 A 141 VAL LEU LYS GLU GLY VAL GLU TYR ARG ILE LYS ILE SER SEQRES 5 A 141 PHE ARG VAL ASN ARG GLU ILE VAL SER GLY MET LYS TYR SEQRES 6 A 141 ILE GLN HIS THR TYR ARG TYR GLY VAL TYR ILE ASP TYR SEQRES 7 A 141 THR ASP TYR MET VAL GLY SER TYR GLY PRO ARG ALA GLU SEQRES 8 A 141 GLU TYR GLU PHE LEU THR PRO VAL GLU GLU ALA PRO LYS SEQRES 9 A 141 GLY MET LEU ALA ARG GLY SER TYR SER ILE LYS SER ARG SEQRES 10 A 141 PHE THR ASP ASP ASP LYS THR ASP HIS LEU SER TRP GLU SEQRES 11 A 141 TRP ASN LEU THR ILE LYS LYS ASP TRP LYS ASP SEQRES 1 B 141 GLY ALA MET VAL PRO ASN VAL VAL VAL THR GLY LEU THR SEQRES 2 B 141 LEU VAL CYS SER SER ALA PRO GLY PRO LEU GLU LEU ASP SEQRES 3 B 141 LEU THR GLY ASP LEU GLU SER PHE LYS LYS GLN SER PHE SEQRES 4 B 141 VAL LEU LYS GLU GLY VAL GLU TYR ARG ILE LYS ILE SER SEQRES 5 B 141 PHE ARG VAL ASN ARG GLU ILE VAL SER GLY MET LYS TYR SEQRES 6 B 141 ILE GLN HIS THR TYR ARG TYR GLY VAL TYR ILE ASP TYR SEQRES 7 B 141 THR ASP TYR MET VAL GLY SER TYR GLY PRO ARG ALA GLU SEQRES 8 B 141 GLU TYR GLU PHE LEU THR PRO VAL GLU GLU ALA PRO LYS SEQRES 9 B 141 GLY MET LEU ALA ARG GLY SER TYR SER ILE LYS SER ARG SEQRES 10 B 141 PHE THR ASP ASP ASP LYS THR ASP HIS LEU SER TRP GLU SEQRES 11 B 141 TRP ASN LEU THR ILE LYS LYS ASP TRP LYS ASP HET FMT A1203 3 HET FMT A1204 3 HET TRS A1205 8 HETNAM FMT FORMIC ACID HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 3 FMT 2(C H2 O2) FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 HOH *213(H2 O) HELIX 1 1 LEU A 94 GLN A 100 5 7 HELIX 2 2 GLY A 168 ARG A 172 5 5 HELIX 3 3 LEU B 94 GLN B 100 5 7 HELIX 4 4 GLY B 168 ARG B 172 5 5 SHEET 1 AA 4 GLU A 87 ASP A 89 0 SHEET 2 AA 4 VAL A 70 VAL A 78 -1 O LEU A 75 N LEU A 88 SHEET 3 AA 4 GLU A 109 VAL A 118 -1 O ARG A 111 N VAL A 78 SHEET 4 AA 4 GLU A 163 GLU A 164 -1 O GLU A 163 N TYR A 110 SHEET 1 AB 4 GLU A 87 ASP A 89 0 SHEET 2 AB 4 VAL A 70 VAL A 78 -1 O LEU A 75 N LEU A 88 SHEET 3 AB 4 GLU A 109 VAL A 118 -1 O ARG A 111 N VAL A 78 SHEET 4 AB 4 TYR A 156 LEU A 159 -1 O TYR A 156 N PHE A 116 SHEET 1 AC 5 PHE A 102 LYS A 105 0 SHEET 2 AC 5 LEU A 190 LYS A 199 1 O ASN A 195 N PHE A 102 SHEET 3 AC 5 GLY A 173 THR A 182 -1 O GLY A 173 N ILE A 198 SHEET 4 AC 5 VAL A 123 ARG A 134 -1 O LYS A 127 N THR A 182 SHEET 5 AC 5 VAL A 137 TYR A 149 -1 O VAL A 137 N ARG A 134 SHEET 1 BA 4 LEU B 86 ASP B 89 0 SHEET 2 BA 4 VAL B 70 VAL B 78 -1 O LEU B 75 N LEU B 88 SHEET 3 BA 4 GLU B 109 VAL B 118 -1 O ARG B 111 N VAL B 78 SHEET 4 BA 4 GLU B 163 GLU B 164 -1 O GLU B 163 N TYR B 110 SHEET 1 BB 4 LEU B 86 ASP B 89 0 SHEET 2 BB 4 VAL B 70 VAL B 78 -1 O LEU B 75 N LEU B 88 SHEET 3 BB 4 GLU B 109 VAL B 118 -1 O ARG B 111 N VAL B 78 SHEET 4 BB 4 ARG B 152 LEU B 159 -1 O ARG B 152 N VAL B 118 SHEET 1 BC 5 PHE B 102 LYS B 105 0 SHEET 2 BC 5 LEU B 190 LYS B 199 1 O ASN B 195 N PHE B 102 SHEET 3 BC 5 GLY B 173 THR B 182 -1 O GLY B 173 N ILE B 198 SHEET 4 BC 5 VAL B 123 ARG B 134 -1 O LYS B 127 N THR B 182 SHEET 5 BC 5 VAL B 137 TYR B 149 -1 O VAL B 137 N ARG B 134 SITE 1 AC1 8 TYR A 110 ILE A 112 GLN A 130 THR A 132 SITE 2 AC1 8 ASP A 140 HOH A2050 HOH A2097 LEU B 170 SITE 1 AC2 6 LYS A 178 SER A 179 ARG A 180 SER A 191 SITE 2 AC2 6 TRP A 192 HOH A2096 SITE 1 AC3 1 VAL A 78 CRYST1 77.308 77.308 171.659 90.00 90.00 120.00 P 31 2 1 12 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 0.012935 0.007468 0.000000 0.00000 SCALE2 0.000000 0.014936 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005826 0.00000