HEADER HYDROLASE 11-FEB-17 5X4B TITLE CRYSTAL STRUCTURE OF N-TERMINAL G-DOMAIN OF ENGA FROM BACILLUS TITLE 2 SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE DER; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 2-163; COMPND 5 SYNONYM: GTP-BINDING PROTEIN ENGA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS (STRAIN 168); SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: DER, ENGA, YPHC, BSU22840; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE2 KEYWDS RIBOSOME BIOGENESIS, ROSSMANN FOLD, GTPASE, GDP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.SINGH,B.PRAKASH REVDAT 4 29-MAY-24 5X4B 1 REMARK REVDAT 3 27-APR-22 5X4B 1 LINK REVDAT 2 25-DEC-19 5X4B 1 REMARK REVDAT 1 31-MAY-17 5X4B 0 SPRSDE 31-MAY-17 5X4B 4KYU JRNL AUTH V.SINGH,B.PRAKASH JRNL TITL CRYSTAL STRUCTURE OF N-TERMINAL G-DOMAIN OF ENGA FROM JRNL TITL 2 BACILLUS SUBTILIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 43793 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2305 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2991 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.1560 REMARK 3 BIN FREE R VALUE SET COUNT : 157 REMARK 3 BIN FREE R VALUE : 0.1970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2224 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 256 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.40000 REMARK 3 B22 (A**2) : -0.42000 REMARK 3 B33 (A**2) : 0.13000 REMARK 3 B12 (A**2) : -0.17000 REMARK 3 B13 (A**2) : -0.32000 REMARK 3 B23 (A**2) : 0.25000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.069 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.951 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2339 ; 0.026 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2112 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3195 ; 2.442 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4869 ; 1.164 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 298 ; 6.610 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;34.890 ;24.554 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 348 ;11.289 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;15.113 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 363 ; 0.148 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2627 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 477 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5X4B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1300002912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 RU300 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46098 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 200 DATA REDUNDANCY : 4.649 REMARK 200 R MERGE (I) : 0.02000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 45.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.72 REMARK 200 R MERGE FOR SHELL (I) : 0.06200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 24.21 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, NH4CL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL 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 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 ILE A 28 REMARK 465 SER A 29 REMARK 465 ILE A 30 REMARK 465 VAL A 31 REMARK 465 GLU A 32 REMARK 465 ASP A 33 REMARK 465 THR A 34 REMARK 465 PRO A 35 REMARK 465 GLY A 36 REMARK 465 VAL A 37 REMARK 465 GLY B 2 REMARK 465 GLY B 25 REMARK 465 GLU B 26 REMARK 465 ARG B 27 REMARK 465 ILE B 28 REMARK 465 SER B 29 REMARK 465 ILE B 30 REMARK 465 VAL B 31 REMARK 465 GLU B 32 REMARK 465 ASP B 33 REMARK 465 THR B 34 REMARK 465 PRO B 35 REMARK 465 GLY B 36 REMARK 465 VAL B 37 REMARK 465 THR B 38 REMARK 465 ARG B 39 REMARK 465 ASP B 40 REMARK 465 ARG B 41 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 3 CE NZ REMARK 470 THR A 38 OG1 CG2 REMARK 470 ARG A 39 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 40 CG OD1 OD2 REMARK 470 ARG A 41 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 ASP A 62 CG OD1 OD2 REMARK 470 ILE A 63 CG1 CG2 CD1 REMARK 470 ASP A 65 CG OD1 OD2 REMARK 470 ILE A 72 CD1 REMARK 470 GLU A 102 OE2 REMARK 470 ARG A 109 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 GLU A 125 CG CD OE1 OE2 REMARK 470 LYS B 3 CG CD CE NZ REMARK 470 GLU B 47 CG CD OE1 OE2 REMARK 470 LEU B 49 CG CD1 CD2 REMARK 470 ASN B 50 CG OD1 ND2 REMARK 470 GLU B 125 CG CD OE1 OE2 REMARK 470 TYR B 131 CG CD1 CD2 CE1 CE2 CZ OH 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 381 O HOH B 400 1.62 REMARK 500 O HOH A 426 O HOH A 433 1.71 REMARK 500 O HOH A 385 O HOH A 415 1.71 REMARK 500 CB ARG A 39 O HOH A 414 1.90 REMARK 500 O HOH B 385 O HOH B 399 1.90 REMARK 500 OD2 ASP B 81 O HOH B 301 1.97 REMARK 500 N ARG B 127 O HOH B 302 1.98 REMARK 500 OH TYR B 43 O HOH B 303 2.04 REMARK 500 O HOH B 307 O HOH B 402 2.07 REMARK 500 O HOH B 399 O HOH B 416 2.11 REMARK 500 O HOH A 348 O HOH A 402 2.12 REMARK 500 O HOH A 417 O HOH A 422 2.16 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 O HOH A 407 O HOH B 301 1455 2.02 REMARK 500 OE2 GLU A 140 O HOH B 301 1455 2.03 REMARK 500 O HOH A 422 O HOH B 388 1455 2.08 REMARK 500 CB ASP A 65 O HOH B 406 1545 2.19 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 ASN A 13 C ASN A 13 O 0.116 REMARK 500 TYR A 142 CE1 TYR A 142 CZ -0.079 REMARK 500 TYR B 43 CB TYR B 43 CG -0.091 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 MET A 80 CG - SD - CE ANGL. DEV. = -13.4 DEGREES REMARK 500 ASP A 81 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP A 84 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 57 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ASP B 62 CB - CG - OD1 ANGL. DEV. = 9.9 DEGREES REMARK 500 ASP B 62 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP B 84 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 LYS B 105 CD - CE - NZ ANGL. DEV. = -15.3 DEGREES REMARK 500 ASP B 122 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 TYR B 134 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 TYR B 134 CD1 - CE1 - CZ ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP B 157 CB - CG - OD1 ANGL. DEV. = 9.4 DEGREES REMARK 500 ASP B 157 CB - CG - OD2 ANGL. DEV. = -6.8 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 ILE A 42 -58.21 74.16 REMARK 500 LEU A 49 -120.96 54.97 REMARK 500 ASP A 65 87.96 -20.29 REMARK 500 LEU B 49 -112.90 51.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 VAL A 14 13.31 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 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 GDP A 201 O2B 87.6 REMARK 620 3 HOH A 334 O 99.4 82.1 REMARK 620 4 HOH A 362 O 96.1 86.9 160.6 REMARK 620 5 HOH A 401 O 92.1 164.6 82.8 108.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 205 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 124 OG1 REMARK 620 2 HOH A 410 O 61.3 REMARK 620 3 HOH B 363 O 134.0 149.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 202 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 346 O REMARK 620 2 HOH A 389 O 89.7 REMARK 620 3 HOH B 362 O 67.0 92.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 10 O REMARK 620 2 GLN B 75 OE1 125.8 REMARK 620 3 HOH B 329 O 91.0 123.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 17 OG REMARK 620 2 GDP B 201 O1B 92.2 REMARK 620 3 HOH B 310 O 90.4 92.6 REMARK 620 4 HOH B 358 O 90.1 90.3 177.1 REMARK 620 5 HOH B 408 O 99.6 167.4 83.0 94.1 REMARK 620 N 1 2 3 4 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 K A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5X4B RELATED DB: PDB DBREF 5X4B A 2 163 UNP P50743 DER_BACSU 2 163 DBREF 5X4B B 2 163 UNP P50743 DER_BACSU 2 163 SEQRES 1 A 162 GLY LYS PRO VAL VAL ALA ILE VAL GLY ARG PRO ASN VAL SEQRES 2 A 162 GLY LYS SER THR ILE PHE ASN ARG ILE ALA GLY GLU ARG SEQRES 3 A 162 ILE SER ILE VAL GLU ASP THR PRO GLY VAL THR ARG ASP SEQRES 4 A 162 ARG ILE TYR SER SER ALA GLU TRP LEU ASN TYR ASP PHE SEQRES 5 A 162 ASN LEU ILE ASP THR GLY GLY ILE ASP ILE GLY ASP GLU SEQRES 6 A 162 PRO PHE LEU ALA GLN ILE ARG GLN GLN ALA GLU ILE ALA SEQRES 7 A 162 MET ASP GLU ALA ASP VAL ILE ILE PHE MET VAL ASN GLY SEQRES 8 A 162 ARG GLU GLY VAL THR ALA ALA ASP GLU GLU VAL ALA LYS SEQRES 9 A 162 ILE LEU TYR ARG THR LYS LYS PRO VAL VAL LEU ALA VAL SEQRES 10 A 162 ASN LYS LEU ASP ASN THR GLU MET ARG ALA ASN ILE TYR SEQRES 11 A 162 ASP PHE TYR SER LEU GLY PHE GLY GLU PRO TYR PRO ILE SEQRES 12 A 162 SER GLY THR HIS GLY LEU GLY LEU GLY ASP LEU LEU ASP SEQRES 13 A 162 ALA VAL ALA GLU HIS PHE SEQRES 1 B 162 GLY LYS PRO VAL VAL ALA ILE VAL GLY ARG PRO ASN VAL SEQRES 2 B 162 GLY LYS SER THR ILE PHE ASN ARG ILE ALA GLY GLU ARG SEQRES 3 B 162 ILE SER ILE VAL GLU ASP THR PRO GLY VAL THR ARG ASP SEQRES 4 B 162 ARG ILE TYR SER SER ALA GLU TRP LEU ASN TYR ASP PHE SEQRES 5 B 162 ASN LEU ILE ASP THR GLY GLY ILE ASP ILE GLY ASP GLU SEQRES 6 B 162 PRO PHE LEU ALA GLN ILE ARG GLN GLN ALA GLU ILE ALA SEQRES 7 B 162 MET ASP GLU ALA ASP VAL ILE ILE PHE MET VAL ASN GLY SEQRES 8 B 162 ARG GLU GLY VAL THR ALA ALA ASP GLU GLU VAL ALA LYS SEQRES 9 B 162 ILE LEU TYR ARG THR LYS LYS PRO VAL VAL LEU ALA VAL SEQRES 10 B 162 ASN LYS LEU ASP ASN THR GLU MET ARG ALA ASN ILE TYR SEQRES 11 B 162 ASP PHE TYR SER LEU GLY PHE GLY GLU PRO TYR PRO ILE SEQRES 12 B 162 SER GLY THR HIS GLY LEU GLY LEU GLY ASP LEU LEU ASP SEQRES 13 B 162 ALA VAL ALA GLU HIS PHE HET GDP A 201 28 HET K A 202 1 HET K A 203 1 HET MG A 204 1 HET K A 205 1 HET GDP B 201 28 HET NA B 202 1 HET MG B 203 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 3 GDP 2(C10 H15 N5 O11 P2) FORMUL 4 K 3(K 1+) FORMUL 6 MG 2(MG 2+) FORMUL 9 NA NA 1+ FORMUL 11 HOH *256(H2 O) HELIX 1 AA1 GLY A 15 ALA A 24 1 10 HELIX 2 AA2 GLY A 59 ILE A 61 5 3 HELIX 3 AA3 PRO A 67 ALA A 83 1 17 HELIX 4 AA4 THR A 97 TYR A 108 1 12 HELIX 5 AA5 ASN A 123 GLY A 137 5 15 HELIX 6 AA6 GLY A 151 HIS A 162 1 12 HELIX 7 AA7 GLY B 15 ALA B 24 1 10 HELIX 8 AA8 GLY B 59 ILE B 61 5 3 HELIX 9 AA9 PRO B 67 ALA B 83 1 17 HELIX 10 AB1 THR B 97 TYR B 108 1 12 HELIX 11 AB2 ASN B 123 GLY B 137 5 15 HELIX 12 AB3 GLY B 151 GLU B 161 1 11 SHEET 1 AA1 6 TYR A 43 TRP A 48 0 SHEET 2 AA1 6 TYR A 51 ASP A 57 -1 O LEU A 55 N SER A 44 SHEET 3 AA1 6 VAL A 5 VAL A 9 1 N ILE A 8 O ILE A 56 SHEET 4 AA1 6 VAL A 85 ASN A 91 1 O ILE A 87 N ALA A 7 SHEET 5 AA1 6 VAL A 114 ASN A 119 1 O VAL A 115 N ILE A 86 SHEET 6 AA1 6 PRO A 141 PRO A 143 1 O TYR A 142 N VAL A 118 SHEET 1 AA2 6 TYR B 43 TRP B 48 0 SHEET 2 AA2 6 TYR B 51 ASP B 57 -1 O LEU B 55 N SER B 44 SHEET 3 AA2 6 VAL B 5 VAL B 9 1 N ILE B 8 O ILE B 56 SHEET 4 AA2 6 VAL B 85 ASN B 91 1 O MET B 89 N VAL B 9 SHEET 5 AA2 6 VAL B 114 ASN B 119 1 O VAL B 115 N ILE B 86 SHEET 6 AA2 6 TYR B 142 PRO B 143 1 O TYR B 142 N VAL B 118 LINK OG ASER A 17 MG MG A 204 1555 1555 1.97 LINK OG1 THR A 124 K K A 205 1555 1555 3.44 LINK O2B GDP A 201 MG MG A 204 1555 1555 2.30 LINK K K A 202 O HOH A 346 1555 1555 3.18 LINK K K A 202 O HOH A 389 1555 1555 3.14 LINK K K A 202 O HOH B 362 1555 1555 3.09 LINK K K A 203 O HOH A 402 1555 1555 2.48 LINK MG MG A 204 O HOH A 334 1555 1555 1.94 LINK MG MG A 204 O HOH A 362 1555 1555 1.85 LINK MG MG A 204 O HOH A 401 1555 1555 2.31 LINK K K A 205 O HOH A 410 1555 1555 3.14 LINK K K A 205 O HOH B 363 1555 1555 3.20 LINK O GLY B 10 NA NA B 202 1555 1555 2.86 LINK OG BSER B 17 MG MG B 203 1555 1555 2.18 LINK OE1 GLN B 75 NA NA B 202 1555 1555 2.73 LINK O1B GDP B 201 MG MG B 203 1555 1555 1.95 LINK NA NA B 202 O HOH B 329 1555 1555 2.74 LINK MG MG B 203 O HOH B 310 1555 1555 1.94 LINK MG MG B 203 O HOH B 358 1555 1555 2.08 LINK MG MG B 203 O HOH B 408 1555 1555 2.18 SITE 1 AC1 25 ASN A 13 VAL A 14 GLY A 15 LYS A 16 SITE 2 AC1 25 SER A 17 THR A 18 ASN A 119 LYS A 120 SITE 3 AC1 25 ASP A 122 SER A 145 GLY A 146 THR A 147 SITE 4 AC1 25 MG A 204 HOH A 306 HOH A 310 HOH A 323 SITE 5 AC1 25 HOH A 329 HOH A 334 HOH A 335 HOH A 342 SITE 6 AC1 25 HOH A 354 HOH A 362 HOH A 364 HOH A 380 SITE 7 AC1 25 HOH A 398 SITE 1 AC2 3 GLY A 153 ALA B 99 HOH B 362 SITE 1 AC3 2 PHE A 163 HOH A 402 SITE 1 AC4 5 SER A 17 GDP A 201 HOH A 334 HOH A 362 SITE 2 AC4 5 HOH A 401 SITE 1 AC5 3 THR A 124 ASN B 91 LYS B 120 SITE 1 AC6 23 ASN B 13 VAL B 14 GLY B 15 LYS B 16 SITE 2 AC6 23 SER B 17 THR B 18 ASN B 119 LYS B 120 SITE 3 AC6 23 ASP B 122 SER B 145 GLY B 146 THR B 147 SITE 4 AC6 23 MG B 203 HOH B 310 HOH B 315 HOH B 316 SITE 5 AC6 23 HOH B 323 HOH B 333 HOH B 350 HOH B 352 SITE 6 AC6 23 HOH B 358 HOH B 359 HOH B 394 SITE 1 AC7 5 GLY B 10 PRO B 12 GLN B 71 GLN B 75 SITE 2 AC7 5 HOH B 329 SITE 1 AC8 5 SER B 17 GDP B 201 HOH B 310 HOH B 358 SITE 2 AC8 5 HOH B 408 CRYST1 42.260 43.750 50.710 66.88 79.88 70.82 P 1 2 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 0.023663 -0.008232 -0.001349 0.00000 SCALE2 0.000000 0.024201 -0.009347 0.00000 SCALE3 0.000000 0.000000 0.021474 0.00000