HEADER HYDROLASE 03-OCT-16 5M04 TITLE STRUCTURE OF OBGE FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE OBGE/CGTA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GTP-BINDING PROTEIN OBG; COMPND 5 EC: 3.6.5.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI DH5[ALPHA]; SOURCE 3 ORGANISM_TAXID: 668369; SOURCE 4 GENE: OBGE, CGTA, OBG, YHBZ, B3183, JW3150; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA, PLYSS KEYWDS GTPASE, OBGE, CGTA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.GKEKAS,R.K.SINGH,W.VERSEES REVDAT 4 17-JAN-24 5M04 1 REMARK REVDAT 3 19-APR-17 5M04 1 JRNL REVDAT 2 08-MAR-17 5M04 1 JRNL REVDAT 1 01-MAR-17 5M04 0 JRNL AUTH S.GKEKAS,R.K.SINGH,A.V.SHKUMATOV,J.MESSENS,M.FAUVART, JRNL AUTH 2 N.VERSTRAETEN,J.MICHIELS,W.VERSEES JRNL TITL STRUCTURAL AND BIOCHEMICAL ANALYSIS OF ESCHERICHIA COLI JRNL TITL 2 OBGE, A CENTRAL REGULATOR OF BACTERIAL PERSISTENCE. JRNL REF J. BIOL. CHEM. V. 292 5871 2017 JRNL REFN ESSN 1083-351X JRNL PMID 28223358 JRNL DOI 10.1074/JBC.M116.761809 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 88.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 39039 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2051 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2845 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.3540 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2570 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.67000 REMARK 3 B22 (A**2) : 1.25000 REMARK 3 B33 (A**2) : -0.58000 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): 0.117 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.112 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.944 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2620 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2529 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3544 ; 1.763 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5827 ; 0.996 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 336 ; 6.793 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;34.640 ;24.486 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 451 ;14.587 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;23.342 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 394 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2955 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 555 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1348 ; 3.858 ; 4.666 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1347 ; 3.858 ; 4.663 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1682 ; 5.416 ; 6.976 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1683 ; 5.416 ; 6.979 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1272 ; 4.533 ; 5.132 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1264 ; 4.542 ; 5.138 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1850 ; 6.872 ; 7.492 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2971 ; 9.611 ;37.803 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2922 ; 9.559 ;37.620 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: NULL REMARK 4 REMARK 4 5M04 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001635. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4.-5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07812 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41090 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 88.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.810 REMARK 200 R MERGE (I) : 0.09028 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.97 REMARK 200 R MERGE FOR SHELL (I) : 2.32600 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: 1LNZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% (W/V) POLYETHYLENE GLYCOL (PEG) REMARK 280 6000, 15% (V/V) 2-PROPANOL AND 100 MM SODIUM CITRATE/HCL PH 5.6., REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.73000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 88.73000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 32.29500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.29500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.50000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 88.73000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.29500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.50000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 88.73000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.29500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.50000 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 SER A 133 REMARK 465 VAL A 134 REMARK 465 ASN A 135 REMARK 465 ARG A 136 REMARK 465 GLN A 339 REMARK 465 ALA A 340 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 24 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 25 CG CD NE CZ NH1 NH2 REMARK 480 GLU A 26 CG CD OE1 OE2 REMARK 480 LYS A 131 CG CD CE NZ REMARK 480 ARG A 139 CG CD NE CZ NH1 NH2 REMARK 480 ASP A 251 C CB CG OD1 OD2 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 LYS A 309 O HOH A 501 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE ARG A 139 CG1 VAL A 291 6554 1.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 24 CB ARG A 24 CG -0.176 REMARK 500 GLU A 26 CB GLU A 26 CG -0.235 REMARK 500 LYS A 131 CB LYS A 131 CG -0.484 REMARK 500 ARG A 139 CB ARG A 139 CG 0.591 REMARK 500 ASP A 251 CA ASP A 251 C 0.757 REMARK 500 ASP A 251 C ASP A 251 O -0.664 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 LYS A 131 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 ARG A 139 CA - CB - CG ANGL. DEV. = -24.9 DEGREES REMARK 500 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 150 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 239 CB - CG - CD ANGL. DEV. = 18.2 DEGREES REMARK 500 ARG A 239 CG - CD - NE ANGL. DEV. = 17.4 DEGREES REMARK 500 ARG A 239 NE - CZ - NH1 ANGL. DEV. = -5.1 DEGREES REMARK 500 ASP A 251 CB - CA - C ANGL. DEV. = -30.5 DEGREES REMARK 500 ASP A 251 CA - CB - CG ANGL. DEV. = -24.4 DEGREES REMARK 500 ASP A 251 CA - C - O ANGL. DEV. = -13.4 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 ASP A 35 18.91 -141.87 REMARK 500 ASP A 204 -173.79 -170.18 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 DBREF 5M04 A 1 340 UNP P42641 OBG_ECOLI 1 340 SEQADV 5M04 MET A -19 UNP P42641 INITIATING METHIONINE SEQADV 5M04 GLY A -18 UNP P42641 EXPRESSION TAG SEQADV 5M04 SER A -17 UNP P42641 EXPRESSION TAG SEQADV 5M04 SER A -16 UNP P42641 EXPRESSION TAG SEQADV 5M04 HIS A -15 UNP P42641 EXPRESSION TAG SEQADV 5M04 HIS A -14 UNP P42641 EXPRESSION TAG SEQADV 5M04 HIS A -13 UNP P42641 EXPRESSION TAG SEQADV 5M04 HIS A -12 UNP P42641 EXPRESSION TAG SEQADV 5M04 HIS A -11 UNP P42641 EXPRESSION TAG SEQADV 5M04 HIS A -10 UNP P42641 EXPRESSION TAG SEQADV 5M04 SER A -9 UNP P42641 EXPRESSION TAG SEQADV 5M04 SER A -8 UNP P42641 EXPRESSION TAG SEQADV 5M04 GLY A -7 UNP P42641 EXPRESSION TAG SEQADV 5M04 LEU A -6 UNP P42641 EXPRESSION TAG SEQADV 5M04 VAL A -5 UNP P42641 EXPRESSION TAG SEQADV 5M04 PRO A -4 UNP P42641 EXPRESSION TAG SEQADV 5M04 ARG A -3 UNP P42641 EXPRESSION TAG SEQADV 5M04 GLY A -2 UNP P42641 EXPRESSION TAG SEQADV 5M04 SER A -1 UNP P42641 EXPRESSION TAG SEQADV 5M04 HIS A 0 UNP P42641 EXPRESSION TAG SEQRES 1 A 360 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 360 LEU VAL PRO ARG GLY SER HIS MET LYS PHE VAL ASP GLU SEQRES 3 A 360 ALA SER ILE LEU VAL VAL ALA GLY ASP GLY GLY ASN GLY SEQRES 4 A 360 CYS VAL SER PHE ARG ARG GLU LYS TYR ILE PRO LYS GLY SEQRES 5 A 360 GLY PRO ASP GLY GLY ASP GLY GLY ASP GLY GLY ASP VAL SEQRES 6 A 360 TRP MET GLU ALA ASP GLU ASN LEU ASN THR LEU ILE ASP SEQRES 7 A 360 TYR ARG PHE GLU LYS SER PHE ARG ALA GLU ARG GLY GLN SEQRES 8 A 360 ASN GLY ALA SER ARG ASP CYS THR GLY LYS ARG GLY LYS SEQRES 9 A 360 ASP VAL THR ILE LYS VAL PRO VAL GLY THR ARG VAL ILE SEQRES 10 A 360 ASP GLN GLY THR GLY GLU THR MET GLY ASP MET THR LYS SEQRES 11 A 360 HIS GLY GLN ARG LEU LEU VAL ALA LYS GLY GLY TRP HIS SEQRES 12 A 360 GLY LEU GLY ASN THR ARG PHE LYS SER SER VAL ASN ARG SEQRES 13 A 360 THR PRO ARG GLN LYS THR ASN GLY THR PRO GLY ASP LYS SEQRES 14 A 360 ARG GLU LEU LEU LEU GLU LEU MET LEU LEU ALA ASP VAL SEQRES 15 A 360 GLY MET LEU GLY MET PRO ASN ALA GLY LYS SER THR PHE SEQRES 16 A 360 ILE ARG ALA VAL SER ALA ALA LYS PRO LYS VAL ALA ASP SEQRES 17 A 360 TYR PRO PHE THR THR LEU VAL PRO SER LEU GLY VAL VAL SEQRES 18 A 360 ARG MET ASP ASN GLU LYS SER PHE VAL VAL ALA ASP ILE SEQRES 19 A 360 PRO GLY LEU ILE GLU GLY ALA ALA GLU GLY ALA GLY LEU SEQRES 20 A 360 GLY ILE ARG PHE LEU LYS HIS LEU GLU ARG CYS ARG VAL SEQRES 21 A 360 LEU LEU HIS LEU ILE ASP ILE ASP PRO ILE ASP GLY THR SEQRES 22 A 360 ASP PRO VAL GLU ASN ALA ARG ILE ILE ILE SER GLU LEU SEQRES 23 A 360 GLU LYS TYR SER GLN ASP LEU ALA THR LYS PRO ARG TRP SEQRES 24 A 360 LEU VAL PHE ASN LYS ILE ASP LEU LEU ASP LYS VAL GLU SEQRES 25 A 360 ALA GLU GLU LYS ALA LYS ALA ILE ALA GLU ALA LEU GLY SEQRES 26 A 360 TRP GLU ASP LYS TYR TYR LEU ILE SER ALA ALA SER GLY SEQRES 27 A 360 LEU GLY VAL LYS ASP LEU CYS TRP ASP VAL MET THR PHE SEQRES 28 A 360 ILE ILE GLU ASN PRO VAL VAL GLN ALA HET GDP A 401 28 HET MG A 402 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 *169(H2 O) HELIX 1 AA1 LEU A 56 PHE A 61 5 6 HELIX 2 AA2 GLY A 126 LYS A 131 5 6 HELIX 3 AA3 GLY A 171 SER A 180 1 10 HELIX 4 AA4 ILE A 214 GLU A 219 1 6 HELIX 5 AA5 ALA A 225 HIS A 234 1 10 HELIX 6 AA6 LEU A 235 CYS A 238 5 4 HELIX 7 AA7 ASP A 254 SER A 270 1 17 HELIX 8 AA8 SER A 270 THR A 275 1 6 HELIX 9 AA9 LYS A 284 LEU A 288 5 5 HELIX 10 AB1 ASP A 289 LEU A 304 1 16 HELIX 11 AB2 GLY A 320 ASN A 335 1 16 SHEET 1 AA1 5 SER A 64 ARG A 66 0 SHEET 2 AA1 5 LYS A 2 VAL A 12 1 N LEU A 10 O PHE A 65 SHEET 3 AA1 5 LYS A 149 MET A 157 -1 O LEU A 156 N ASP A 5 SHEET 4 AA1 5 THR A 94 ASP A 98 -1 N ILE A 97 O LEU A 153 SHEET 5 AA1 5 THR A 104 MET A 108 -1 O GLY A 106 N VAL A 96 SHEET 1 AA2 3 SER A 64 ARG A 66 0 SHEET 2 AA2 3 LYS A 2 VAL A 12 1 N LEU A 10 O PHE A 65 SHEET 3 AA2 3 LYS A 185 ALA A 187 -1 O LYS A 185 N VAL A 4 SHEET 1 AA3 3 VAL A 86 VAL A 90 0 SHEET 2 AA3 3 VAL A 45 ALA A 49 1 N TRP A 46 O VAL A 86 SHEET 3 AA3 3 ARG A 114 ALA A 118 -1 O LEU A 115 N MET A 47 SHEET 1 AA4 6 LEU A 198 ASP A 204 0 SHEET 2 AA4 6 LYS A 207 ASP A 213 -1 O PHE A 209 N VAL A 201 SHEET 3 AA4 6 VAL A 162 LEU A 165 1 N MET A 164 O ALA A 212 SHEET 4 AA4 6 VAL A 240 ASP A 246 1 O LEU A 242 N GLY A 163 SHEET 5 AA4 6 ARG A 278 ASN A 283 1 O TRP A 279 N HIS A 243 SHEET 6 AA4 6 TYR A 311 LEU A 312 1 O TYR A 311 N PHE A 282 LINK O1B GDP A 401 MG MG A 402 1555 1555 2.81 SITE 1 AC1 18 ASN A 169 ALA A 170 GLY A 171 LYS A 172 SITE 2 AC1 18 SER A 173 THR A 174 ARG A 177 LYS A 183 SITE 3 AC1 18 ASN A 283 LYS A 284 ASP A 286 LEU A 287 SITE 4 AC1 18 SER A 314 ALA A 315 ALA A 316 MG A 402 SITE 5 AC1 18 HOH A 550 HOH A 566 SITE 1 AC2 4 SER A 173 ARG A 177 LYS A 183 GDP A 401 CRYST1 64.590 83.000 177.460 90.00 90.00 90.00 C 2 2 21 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 0.015482 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012048 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005635 0.00000