HEADER HYDROLASE 04-DEC-08 3FFU TITLE STRUCTURE OF THE RNA PYROPHOSPHOHYDROLASE BDRPPH IN COMPLEX WITH GTP TITLE 2 AND MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE PYROPHOSPHOHYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.6.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BDELLOVIBRIO BACTERIOVORUS; SOURCE 3 ORGANISM_TAXID: 959; SOURCE 4 STRAIN: HD100; SOURCE 5 GENE: BD0714, MUTT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS NUDIX, RNA PYROPHOSPHOHYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.A.MESSING,S.B.GABELLI,L.M.AMZEL REVDAT 4 21-FEB-24 3FFU 1 REMARK LINK REVDAT 3 04-APR-18 3FFU 1 REMARK REVDAT 2 01-NOV-17 3FFU 1 REMARK REVDAT 1 24-MAR-09 3FFU 0 JRNL AUTH S.A.MESSING,S.B.GABELLI,Q.LIU,H.CELESNIK,J.G.BELASCO, JRNL AUTH 2 S.A.PINEIRO,L.M.AMZEL JRNL TITL STRUCTURE AND BIOLOGICAL FUNCTION OF THE RNA JRNL TITL 2 PYROPHOSPHOHYDROLASE BDRPPH FROM BDELLOVIBRIO BACTERIOVORUS. JRNL REF STRUCTURE V. 17 472 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19278661 JRNL DOI 10.1016/J.STR.2008.12.022 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 11171 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.301 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 547 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 785 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 47 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2165 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.87000 REMARK 3 B22 (A**2) : 2.28000 REMARK 3 B33 (A**2) : -4.15000 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): 0.764 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.397 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.306 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 30.027 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2310 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3115 ; 1.393 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 264 ; 7.828 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;37.091 ;24.128 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 397 ;19.483 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;23.907 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 315 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1723 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 883 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1455 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 91 ; 0.150 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 11 ; 0.194 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 24 ; 0.144 ; 0.200 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): 1358 ; 0.369 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2101 ; 0.711 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1133 ; 1.259 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1014 ; 2.063 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3FFU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000050538. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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 : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11207 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.4430 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.71400 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, NA ACETATE, PH 7, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 34.36600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.53450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.37450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.53450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.36600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.37450 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 THR A 2 REMARK 465 ASP A 3 REMARK 465 ASP A 4 REMARK 465 SER A 5 REMARK 465 ALA A 6 REMARK 465 VAL A 7 REMARK 465 GLU A 8 REMARK 465 SER A 9 REMARK 465 LYS A 10 REMARK 465 GLN A 11 REMARK 465 LYS A 12 REMARK 465 LYS A 13 REMARK 465 SER A 14 REMARK 465 LYS A 15 REMARK 465 ILE A 16 REMARK 465 ARG A 17 REMARK 465 LYS A 18 REMARK 465 ARG A 152 REMARK 465 LYS A 153 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ASP B 3 REMARK 465 ASP B 4 REMARK 465 SER B 5 REMARK 465 ALA B 6 REMARK 465 VAL B 7 REMARK 465 GLU B 8 REMARK 465 SER B 9 REMARK 465 LYS B 10 REMARK 465 GLN B 11 REMARK 465 LYS B 12 REMARK 465 LYS B 13 REMARK 465 SER B 14 REMARK 465 LYS B 15 REMARK 465 ILE B 16 REMARK 465 ARG B 17 REMARK 465 LYS B 18 REMARK 465 GLY B 19 REMARK 465 LYS B 153 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 MG MG A 155 O HOH A 161 1.65 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 GLU A 150 C GLU A 150 O 0.130 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 LEU A 46 N - CA - C ANGL. DEV. = -16.6 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 HIS A 20 139.32 167.96 REMARK 500 HIS B 115 -41.57 -133.11 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 SER A 45 LEU A 46 133.97 REMARK 500 SER B 45 LEU B 46 125.08 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 156 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 54 O REMARK 620 2 GLU A 74 OE2 79.9 REMARK 620 3 HOH A 157 O 79.6 106.8 REMARK 620 4 HOH A 158 O 162.7 105.3 83.1 REMARK 620 5 GTP A4033 O2B 73.5 83.6 149.0 123.1 REMARK 620 6 GTP A4033 O1A 85.1 152.6 92.7 95.8 70.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 154 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 70 OE2 REMARK 620 2 HOH A 161 O 121.7 REMARK 620 3 HOH A 162 O 79.9 147.8 REMARK 620 4 GTP A4033 O1B 107.4 73.8 77.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 155 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 70 OE1 REMARK 620 2 GLU A 74 OE2 80.4 REMARK 620 3 HOH A 159 O 156.1 78.6 REMARK 620 4 HOH A 160 O 84.4 82.8 82.0 REMARK 620 5 GTP A4033 O2B 83.9 83.5 104.7 163.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 156 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 54 O REMARK 620 2 GLU B 74 OE1 83.8 REMARK 620 3 HOH B 157 O 76.9 101.7 REMARK 620 4 HOH B 158 O 165.3 98.8 88.4 REMARK 620 5 GTP B4032 O2B 80.4 83.7 155.9 114.2 REMARK 620 6 GTP B4032 O1A 93.3 159.9 96.9 88.9 76.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 154 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 70 OE2 REMARK 620 2 HOH B 162 O 78.1 REMARK 620 3 HOH B 163 O 152.1 93.6 REMARK 620 4 GTP B4032 O1B 85.6 86.7 67.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 155 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 70 OE1 REMARK 620 2 HOH B 159 O 129.7 REMARK 620 3 HOH B 160 O 84.3 79.3 REMARK 620 4 GTP B4032 O2B 83.8 84.8 147.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP B4032 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A4033 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 154 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 154 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 156 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EEU RELATED DB: PDB REMARK 900 RELATED ID: 3EES RELATED DB: PDB REMARK 900 RELATED ID: 3EF5 RELATED DB: PDB DBREF 3FFU A 1 153 UNP Q6MPX4 Q6MPX4_BDEBA 1 153 DBREF 3FFU B 1 153 UNP Q6MPX4 Q6MPX4_BDEBA 1 153 SEQRES 1 A 153 MET THR ASP ASP SER ALA VAL GLU SER LYS GLN LYS LYS SEQRES 2 A 153 SER LYS ILE ARG LYS GLY HIS TRP ILE PRO VAL VAL ALA SEQRES 3 A 153 GLY PHE LEU ARG LYS ASP GLY LYS ILE LEU VAL GLY GLN SEQRES 4 A 153 ARG PRO GLU ASN ASN SER LEU ALA GLY GLN TRP GLU PHE SEQRES 5 A 153 PRO GLY GLY LYS ILE GLU ASN GLY GLU THR PRO GLU GLU SEQRES 6 A 153 ALA LEU ALA ARG GLU LEU ASN GLU GLU LEU GLY ILE GLU SEQRES 7 A 153 ALA GLU VAL GLY GLU LEU LYS LEU ALA CYS THR HIS SER SEQRES 8 A 153 TYR GLY ASP VAL GLY ILE LEU ILE LEU PHE TYR GLU ILE SEQRES 9 A 153 LEU TYR TRP LYS GLY GLU PRO ARG ALA LYS HIS HIS MET SEQRES 10 A 153 MET LEU GLU TRP ILE HIS PRO GLU GLU LEU LYS HIS ARG SEQRES 11 A 153 ASN ILE PRO GLU ALA ASN ARG LYS ILE LEU HIS LYS ILE SEQRES 12 A 153 TYR LYS ALA LEU GLY LEU GLU TRP ARG LYS SEQRES 1 B 153 MET THR ASP ASP SER ALA VAL GLU SER LYS GLN LYS LYS SEQRES 2 B 153 SER LYS ILE ARG LYS GLY HIS TRP ILE PRO VAL VAL ALA SEQRES 3 B 153 GLY PHE LEU ARG LYS ASP GLY LYS ILE LEU VAL GLY GLN SEQRES 4 B 153 ARG PRO GLU ASN ASN SER LEU ALA GLY GLN TRP GLU PHE SEQRES 5 B 153 PRO GLY GLY LYS ILE GLU ASN GLY GLU THR PRO GLU GLU SEQRES 6 B 153 ALA LEU ALA ARG GLU LEU ASN GLU GLU LEU GLY ILE GLU SEQRES 7 B 153 ALA GLU VAL GLY GLU LEU LYS LEU ALA CYS THR HIS SER SEQRES 8 B 153 TYR GLY ASP VAL GLY ILE LEU ILE LEU PHE TYR GLU ILE SEQRES 9 B 153 LEU TYR TRP LYS GLY GLU PRO ARG ALA LYS HIS HIS MET SEQRES 10 B 153 MET LEU GLU TRP ILE HIS PRO GLU GLU LEU LYS HIS ARG SEQRES 11 B 153 ASN ILE PRO GLU ALA ASN ARG LYS ILE LEU HIS LYS ILE SEQRES 12 B 153 TYR LYS ALA LEU GLY LEU GLU TRP ARG LYS HET GTP A4033 32 HET MG A 154 1 HET MG A 155 1 HET MG A 156 1 HET GTP B4032 32 HET MG B 154 1 HET MG B 155 1 HET MG B 156 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 GTP 2(C10 H16 N5 O14 P3) FORMUL 4 MG 6(MG 2+) FORMUL 11 HOH *18(H2 O) HELIX 1 1 THR A 62 GLY A 76 1 15 HELIX 2 2 HIS A 123 ARG A 130 5 8 HELIX 3 3 PRO A 133 LYS A 138 1 6 HELIX 4 4 ILE A 139 GLY A 148 1 10 HELIX 5 5 THR B 62 GLY B 76 1 15 HELIX 6 6 HIS B 123 ARG B 130 5 8 HELIX 7 7 PRO B 133 LYS B 138 1 6 HELIX 8 8 ILE B 139 LEU B 147 1 9 SHEET 1 A 5 TRP A 50 GLU A 51 0 SHEET 2 A 5 LYS A 34 GLN A 39 -1 N GLY A 38 O GLU A 51 SHEET 3 A 5 TRP A 21 LYS A 31 -1 N LYS A 31 O LYS A 34 SHEET 4 A 5 VAL A 95 ILE A 104 1 O LEU A 98 N VAL A 24 SHEET 5 A 5 LEU A 84 TYR A 92 -1 N LYS A 85 O PHE A 101 SHEET 1 B 4 GLY A 54 LYS A 56 0 SHEET 2 B 4 TRP A 21 LYS A 31 -1 N VAL A 25 O GLY A 55 SHEET 3 B 4 LYS A 34 GLN A 39 -1 O LYS A 34 N LYS A 31 SHEET 4 B 4 LEU A 119 ILE A 122 -1 O ILE A 122 N ILE A 35 SHEET 1 C 2 GLU A 78 GLU A 80 0 SHEET 2 C 2 TYR A 106 LYS A 108 -1 O TYR A 106 N GLU A 80 SHEET 1 D 4 GLY B 54 LYS B 56 0 SHEET 2 D 4 TRP B 21 PHE B 28 -1 N VAL B 25 O GLY B 55 SHEET 3 D 4 VAL B 95 GLU B 103 1 O LEU B 98 N VAL B 24 SHEET 4 D 4 LEU B 84 TYR B 92 -1 N LYS B 85 O PHE B 101 SHEET 1 E 3 ARG B 30 LYS B 31 0 SHEET 2 E 3 LYS B 34 GLN B 39 -1 O LYS B 34 N LYS B 31 SHEET 3 E 3 TRP B 50 GLU B 51 -1 O GLU B 51 N GLY B 38 SHEET 1 F 3 ARG B 30 LYS B 31 0 SHEET 2 F 3 LYS B 34 GLN B 39 -1 O LYS B 34 N LYS B 31 SHEET 3 F 3 LEU B 119 ILE B 122 -1 O ILE B 122 N ILE B 35 SHEET 1 G 2 GLU B 78 GLU B 80 0 SHEET 2 G 2 TYR B 106 LYS B 108 -1 O TYR B 106 N GLU B 80 LINK O GLY A 54 MG MG A 156 1555 1555 2.19 LINK OE2 GLU A 70 MG MG A 154 1555 1555 2.17 LINK OE1 GLU A 70 MG MG A 155 1555 1555 2.17 LINK OE2 GLU A 74 MG MG A 155 1555 1555 2.18 LINK OE2 GLU A 74 MG MG A 156 1555 1555 2.18 LINK MG MG A 154 O HOH A 161 1555 1555 1.76 LINK MG MG A 154 O HOH A 162 1555 1555 2.00 LINK MG MG A 154 O1B GTP A4033 1555 1555 2.17 LINK MG MG A 155 O HOH A 159 1555 1555 1.98 LINK MG MG A 155 O HOH A 160 1555 1555 1.84 LINK MG MG A 155 O2B GTP A4033 1555 1555 2.17 LINK MG MG A 156 O HOH A 157 1555 1555 1.95 LINK MG MG A 156 O HOH A 158 1555 1555 2.21 LINK MG MG A 156 O2B GTP A4033 1555 1555 2.17 LINK MG MG A 156 O1A GTP A4033 1555 1555 2.16 LINK O GLY B 54 MG MG B 156 1555 1555 2.18 LINK OE2 GLU B 70 MG MG B 154 1555 1555 2.17 LINK OE1 GLU B 70 MG MG B 155 1555 1555 2.17 LINK OE1 GLU B 74 MG MG B 156 1555 1555 2.17 LINK MG MG B 154 O HOH B 162 1555 1555 1.94 LINK MG MG B 154 O HOH B 163 1555 1555 2.42 LINK MG MG B 154 O1B GTP B4032 1555 1555 2.18 LINK MG MG B 155 O HOH B 159 1555 1555 1.82 LINK MG MG B 155 O HOH B 160 1555 1555 1.94 LINK MG MG B 155 O2B GTP B4032 1555 1555 2.17 LINK MG MG B 156 O HOH B 157 1555 1555 2.02 LINK MG MG B 156 O HOH B 158 1555 1555 1.78 LINK MG MG B 156 O2B GTP B4032 1555 1555 2.17 LINK MG MG B 156 O1A GTP B4032 1555 1555 2.17 SITE 1 AC1 24 VAL B 24 ARG B 40 ASN B 44 LEU B 46 SITE 2 AC1 24 GLU B 51 PHE B 52 GLY B 54 GLY B 55 SITE 3 AC1 24 LYS B 56 GLU B 70 GLU B 74 ILE B 97 SITE 4 AC1 24 ILE B 99 PRO B 133 ASN B 136 MG B 154 SITE 5 AC1 24 MG B 155 MG B 156 HOH B 157 HOH B 158 SITE 6 AC1 24 HOH B 159 HOH B 161 HOH B 162 HOH B 163 SITE 1 AC2 23 VAL A 24 ARG A 40 ASN A 44 LEU A 46 SITE 2 AC2 23 GLU A 51 PHE A 52 GLY A 54 GLY A 55 SITE 3 AC2 23 LYS A 56 GLU A 70 GLU A 74 TYR A 92 SITE 4 AC2 23 ILE A 97 PRO A 133 ASN A 136 MG A 154 SITE 5 AC2 23 MG A 155 MG A 156 HOH A 157 HOH A 159 SITE 6 AC2 23 HOH A 161 HOH A 162 HOH A 163 SITE 1 AC3 7 GLU A 70 GLU A 73 MG A 155 HOH A 161 SITE 2 AC3 7 HOH A 162 HOH A 163 GTP A4033 SITE 1 AC4 8 GLU A 70 GLU A 74 MG A 154 MG A 156 SITE 2 AC4 8 HOH A 159 HOH A 160 HOH A 161 GTP A4033 SITE 1 AC5 6 GLY A 54 GLU A 74 MG A 155 HOH A 157 SITE 2 AC5 6 HOH A 158 GTP A4033 SITE 1 AC6 7 GLU B 70 GLU B 73 MG B 155 HOH B 161 SITE 2 AC6 7 HOH B 162 HOH B 163 GTP B4032 SITE 1 AC7 9 GLU B 70 GLU B 73 GLU B 74 MG B 154 SITE 2 AC7 9 MG B 156 HOH B 159 HOH B 160 HOH B 161 SITE 3 AC7 9 GTP B4032 SITE 1 AC8 7 GLY B 54 GLU B 74 MG B 155 HOH B 157 SITE 2 AC8 7 HOH B 158 HOH B 159 GTP B4032 CRYST1 68.732 68.749 93.069 90.00 90.00 90.00 P 21 21 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 0.014549 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014546 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010745 0.00000