HEADER TRANSFERASE 14-AUG-09 3IOM TITLE CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH 2'-DEOXYGUANOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PURINE NUCLEOSIDE PHOSPHORYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PNP, INOSINE PHOSPHORYLASE; COMPND 5 EC: 2.4.2.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 STRAIN: MYCOBACTERIUM TUBERCULOSIS; SOURCE 5 GENE: DEOD, MT3406, MTV016.06, PUNA, PUNA (DEOD) (RV3307) (MT3406) SOURCE 6 (MTV016.06), RV3307; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PURINE NUCLEOSIDE PHOSPHORYLASE, MYCOBACTERIUM TUBERCULOSIS, 2 - KEYWDS 2 DEOXYGUANOSINE, GLYCOSYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.F.DE AZEVEDO JR.,L.A.BASSO,D.S.SANTOS REVDAT 3 06-SEP-23 3IOM 1 REMARK REVDAT 2 22-JUN-11 3IOM 1 JRNL REVDAT 1 12-JAN-11 3IOM 0 JRNL AUTH R.G.DUCATI,L.A.BASSO,D.S.SANTOS,W.F.DE AZEVEDO JRNL TITL CRYSTALLOGRAPHIC AND DOCKING STUDIES OF PURINE NUCLEOSIDE JRNL TITL 2 PHOSPHORYLASE FROM MYCOBACTERIUM TUBERCULOSIS. JRNL REF BIOORG.MED.CHEM. V. 18 4769 2010 JRNL REFN ISSN 0968-0896 JRNL PMID 20570524 JRNL DOI 10.1016/J.BMC.2010.05.009 REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 21023 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1134 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) : 2.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1406 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.1690 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.2550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3792 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 209 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.352 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.239 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.870 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3914 ; 0.022 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5362 ; 1.976 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 522 ; 7.205 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 146 ;38.750 ;22.740 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 556 ;16.849 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;20.874 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 640 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2984 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2228 ; 0.252 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2684 ; 0.319 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 324 ; 0.193 ; 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): 146 ; 0.237 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.207 ; 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): 2598 ; 1.023 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4132 ; 1.780 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1316 ; 2.904 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1230 ; 4.563 ; 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 : 1.20 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 3IOM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054670. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : D03B-MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.42800 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22163 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 REMARK 200 RESOLUTION RANGE LOW (A) : 28.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : 0.08600 REMARK 200 FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.13800 REMARK 200 R SYM FOR SHELL (I) : 0.13800 REMARK 200 FOR SHELL : 3.500 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: 1G2O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PROTEIN WAS COCRYSTALLIZED WITH A REMARK 280 1:0.5:1 STOICHIOMETRY OF 500 MM NA2SO4 (MERCK) AND 3 MM 2DGUO REMARK 280 (FLUKA BIOCHEMIKA), RESPECTIVELY, BY HANGING-DROP VAPOR REMARK 280 DIFFUSION AT 18 C. MTPNP PROTEIN (1 L OF 25 MG ML-1 IN 50 MM REMARK 280 TRIS(HYDROXYMETHYL)AMINOMETHANE (TRIS) PH 7.6) HAD BEEN REMARK 280 PREVIOUSLY MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION REMARK 280 CONTAINING 100 MM TRIS PH 8.0, 25% POLY(ETHYLENE GLYCOL) (PEG) REMARK 280 3350, AND 25 MM MGCL2 AND HANGING DROPS (3.5 L) WERE REMARK 280 EQUILIBRATED AGAINST 400 L OF THE RESERVOIR SOLUTION. , VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 56.74000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.75885 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.33700 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 56.74000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 32.75885 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.33700 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 56.74000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 32.75885 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.33700 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.51771 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 56.67400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 65.51771 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 56.67400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 65.51771 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 56.67400 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 300 REMARK: 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 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 BIOMT1 2 -0.500000 -0.866025 0.000000 56.74000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -98.27656 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 113.48000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 56.74000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -98.27656 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 113.48000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 PRO A 4 REMARK 465 ARG A 5 REMARK 465 PRO A 6 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASP B 3 REMARK 465 PRO B 4 REMARK 465 ARG B 5 REMARK 465 PRO B 6 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 ASP A 29 CB ASP A 29 CG 0.241 REMARK 500 GLU A 152 CG GLU A 152 CD 0.103 REMARK 500 GLU A 166 CB GLU A 166 CG 0.156 REMARK 500 GLU A 166 CG GLU A 166 CD 0.103 REMARK 500 GLU A 245 CG GLU A 245 CD 0.092 REMARK 500 GLU B 166 CB GLU B 166 CG 0.114 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 81 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 LEU A 135 CB - CG - CD1 ANGL. DEV. = -10.9 DEGREES REMARK 500 ARG A 217 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 217 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 LEU B 11 CA - CB - CG ANGL. DEV. = 14.3 DEGREES REMARK 500 ARG B 13 NE - CZ - NH2 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 108 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 125 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG B 217 NE - CZ - NH2 ANGL. DEV. = -3.1 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 THR A 64 -148.60 -100.10 REMARK 500 ALA A 65 84.61 12.56 REMARK 500 HIS A 68 73.39 -68.52 REMARK 500 ALA A 69 171.63 -40.83 REMARK 500 ALA A 79 39.33 -88.66 REMARK 500 SER A 208 -151.92 -145.00 REMARK 500 THR A 209 -44.38 71.89 REMARK 500 ALA B 55 -57.00 -20.54 REMARK 500 VAL B 61 90.35 -68.95 REMARK 500 THR B 64 104.48 -24.55 REMARK 500 ALA B 65 173.74 164.48 REMARK 500 ALA B 66 -137.24 106.00 REMARK 500 HIS B 68 -150.12 -149.88 REMARK 500 ALA B 69 -164.82 -165.30 REMARK 500 SER B 161 113.23 -35.95 REMARK 500 SER B 208 -152.28 -150.68 REMARK 500 THR B 209 -49.57 71.37 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 SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNG A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNG B 801 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G2O RELATED DB: PDB DBREF 3IOM A 1 268 UNP P0A538 PUNA_MYCTU 1 268 DBREF 3IOM B 1 268 UNP P0A538 PUNA_MYCTU 1 268 SEQRES 1 A 268 MET ALA ASP PRO ARG PRO ASP PRO ASP GLU LEU ALA ARG SEQRES 2 A 268 ARG ALA ALA GLN VAL ILE ALA ASP ARG THR GLY ILE GLY SEQRES 3 A 268 GLU HIS ASP VAL ALA VAL VAL LEU GLY SER GLY TRP LEU SEQRES 4 A 268 PRO ALA VAL ALA ALA LEU GLY SER PRO THR THR VAL LEU SEQRES 5 A 268 PRO GLN ALA GLU LEU PRO GLY PHE VAL PRO PRO THR ALA SEQRES 6 A 268 ALA GLY HIS ALA GLY GLU LEU LEU SER VAL PRO ILE GLY SEQRES 7 A 268 ALA HIS ARG VAL LEU VAL LEU ALA GLY ARG ILE HIS ALA SEQRES 8 A 268 TYR GLU GLY HIS ASP LEU ARG TYR VAL VAL HIS PRO VAL SEQRES 9 A 268 ARG ALA ALA ARG ALA ALA GLY ALA GLN ILE MET VAL LEU SEQRES 10 A 268 THR ASN ALA ALA GLY GLY LEU ARG ALA ASP LEU GLN VAL SEQRES 11 A 268 GLY GLN PRO VAL LEU ILE SER ASP HIS LEU ASN LEU THR SEQRES 12 A 268 ALA ARG SER PRO LEU VAL GLY GLY GLU PHE VAL ASP LEU SEQRES 13 A 268 THR ASP ALA TYR SER PRO ARG LEU ARG GLU LEU ALA ARG SEQRES 14 A 268 GLN SER ASP PRO GLN LEU ALA GLU GLY VAL TYR ALA GLY SEQRES 15 A 268 LEU PRO GLY PRO HIS TYR GLU THR PRO ALA GLU ILE ARG SEQRES 16 A 268 MET LEU GLN THR LEU GLY ALA ASP LEU VAL GLY MET SER SEQRES 17 A 268 THR VAL HIS GLU THR ILE ALA ALA ARG ALA ALA GLY ALA SEQRES 18 A 268 GLU VAL LEU GLY VAL SER LEU VAL THR ASN LEU ALA ALA SEQRES 19 A 268 GLY ILE THR GLY GLU PRO LEU SER HIS ALA GLU VAL LEU SEQRES 20 A 268 ALA ALA GLY ALA ALA SER ALA THR ARG MET GLY ALA LEU SEQRES 21 A 268 LEU ALA ASP VAL ILE ALA ARG PHE SEQRES 1 B 268 MET ALA ASP PRO ARG PRO ASP PRO ASP GLU LEU ALA ARG SEQRES 2 B 268 ARG ALA ALA GLN VAL ILE ALA ASP ARG THR GLY ILE GLY SEQRES 3 B 268 GLU HIS ASP VAL ALA VAL VAL LEU GLY SER GLY TRP LEU SEQRES 4 B 268 PRO ALA VAL ALA ALA LEU GLY SER PRO THR THR VAL LEU SEQRES 5 B 268 PRO GLN ALA GLU LEU PRO GLY PHE VAL PRO PRO THR ALA SEQRES 6 B 268 ALA GLY HIS ALA GLY GLU LEU LEU SER VAL PRO ILE GLY SEQRES 7 B 268 ALA HIS ARG VAL LEU VAL LEU ALA GLY ARG ILE HIS ALA SEQRES 8 B 268 TYR GLU GLY HIS ASP LEU ARG TYR VAL VAL HIS PRO VAL SEQRES 9 B 268 ARG ALA ALA ARG ALA ALA GLY ALA GLN ILE MET VAL LEU SEQRES 10 B 268 THR ASN ALA ALA GLY GLY LEU ARG ALA ASP LEU GLN VAL SEQRES 11 B 268 GLY GLN PRO VAL LEU ILE SER ASP HIS LEU ASN LEU THR SEQRES 12 B 268 ALA ARG SER PRO LEU VAL GLY GLY GLU PHE VAL ASP LEU SEQRES 13 B 268 THR ASP ALA TYR SER PRO ARG LEU ARG GLU LEU ALA ARG SEQRES 14 B 268 GLN SER ASP PRO GLN LEU ALA GLU GLY VAL TYR ALA GLY SEQRES 15 B 268 LEU PRO GLY PRO HIS TYR GLU THR PRO ALA GLU ILE ARG SEQRES 16 B 268 MET LEU GLN THR LEU GLY ALA ASP LEU VAL GLY MET SER SEQRES 17 B 268 THR VAL HIS GLU THR ILE ALA ALA ARG ALA ALA GLY ALA SEQRES 18 B 268 GLU VAL LEU GLY VAL SER LEU VAL THR ASN LEU ALA ALA SEQRES 19 B 268 GLY ILE THR GLY GLU PRO LEU SER HIS ALA GLU VAL LEU SEQRES 20 B 268 ALA ALA GLY ALA ALA SER ALA THR ARG MET GLY ALA LEU SEQRES 21 B 268 LEU ALA ASP VAL ILE ALA ARG PHE HET SO4 A 301 5 HET GNG A 800 19 HET SO4 B 302 5 HET GNG B 801 19 HETNAM SO4 SULFATE ION HETNAM GNG 2'-DEOXY-GUANOSINE FORMUL 3 SO4 2(O4 S 2-) FORMUL 4 GNG 2(C10 H13 N5 O4) FORMUL 7 HOH *209(H2 O) HELIX 1 1 ASP A 7 GLY A 24 1 18 HELIX 2 2 TRP A 38 PRO A 40 5 3 HELIX 3 3 ALA A 41 GLY A 46 1 6 HELIX 4 4 ALA A 55 LEU A 57 5 3 HELIX 5 5 HIS A 90 GLY A 94 5 5 HELIX 6 6 ASP A 96 ALA A 110 1 15 HELIX 7 7 SER A 161 ASP A 172 1 12 HELIX 8 8 THR A 190 GLY A 201 1 12 HELIX 9 9 THR A 209 ALA A 219 1 11 HELIX 10 10 SER A 242 PHE A 268 1 27 HELIX 11 11 ASP B 7 GLY B 24 1 18 HELIX 12 12 TRP B 38 PRO B 40 5 3 HELIX 13 13 ALA B 41 GLY B 46 1 6 HELIX 14 14 ALA B 55 LEU B 57 5 3 HELIX 15 15 HIS B 90 GLY B 94 5 5 HELIX 16 16 ASP B 96 VAL B 101 1 6 HELIX 17 17 VAL B 101 ALA B 110 1 10 HELIX 18 18 SER B 161 ASP B 172 1 12 HELIX 19 19 THR B 190 LEU B 200 1 11 HELIX 20 20 THR B 209 ALA B 219 1 11 HELIX 21 21 SER B 242 PHE B 268 1 27 SHEET 1 A10 THR A 50 PRO A 53 0 SHEET 2 A10 GLU A 71 ILE A 77 -1 O LEU A 72 N LEU A 52 SHEET 3 A10 HIS A 80 ALA A 86 -1 O VAL A 84 N LEU A 73 SHEET 4 A10 VAL A 30 VAL A 33 1 N VAL A 32 O LEU A 85 SHEET 5 A10 ILE A 114 GLY A 123 1 O VAL A 116 N ALA A 31 SHEET 6 A10 GLU A 222 LEU A 232 1 O GLU A 222 N MET A 115 SHEET 7 A10 PRO A 133 ASN A 141 -1 N VAL A 134 O SER A 227 SHEET 8 A10 ALA A 176 GLY A 182 1 O GLY A 182 N LEU A 140 SHEET 9 A10 LEU A 204 GLY A 206 1 O GLY A 206 N ALA A 181 SHEET 10 A10 ILE A 114 GLY A 123 -1 N GLY A 122 O VAL A 205 SHEET 1 B10 THR B 50 PRO B 53 0 SHEET 2 B10 GLU B 71 ILE B 77 -1 O LEU B 72 N LEU B 52 SHEET 3 B10 HIS B 80 ALA B 86 -1 O VAL B 84 N LEU B 73 SHEET 4 B10 VAL B 30 LEU B 34 1 N VAL B 32 O LEU B 85 SHEET 5 B10 ILE B 114 GLY B 123 1 O VAL B 116 N VAL B 33 SHEET 6 B10 GLU B 222 LEU B 232 1 O LEU B 228 N ASN B 119 SHEET 7 B10 PRO B 133 ASN B 141 -1 N VAL B 134 O SER B 227 SHEET 8 B10 ALA B 176 GLY B 182 1 O GLY B 182 N LEU B 140 SHEET 9 B10 LEU B 204 GLY B 206 1 O LEU B 204 N ALA B 181 SHEET 10 B10 ILE B 114 GLY B 123 -1 N GLY B 122 O VAL B 205 CISPEP 1 GLY A 185 PRO A 186 0 4.11 CISPEP 2 GLY B 185 PRO B 186 0 4.94 SITE 1 AC1 9 GLY A 35 SER A 36 ARG A 88 HIS A 90 SITE 2 AC1 9 THR A 118 ASN A 119 SER A 208 HOH A 334 SITE 3 AC1 9 GNG A 800 SITE 1 AC2 15 SER A 36 ALA A 120 GLY A 122 TYR A 188 SITE 2 AC2 15 GLU A 189 VAL A 205 GLY A 206 MET A 207 SITE 3 AC2 15 THR A 230 ASN A 231 LEU A 241 HIS A 243 SITE 4 AC2 15 VAL A 246 SO4 A 301 HOH A 369 SITE 1 AC3 10 GLY B 35 SER B 36 ARG B 88 HIS B 90 SITE 2 AC3 10 ASN B 119 ALA B 120 SER B 208 HOH B 296 SITE 3 AC3 10 HOH B 299 GNG B 801 SITE 1 AC4 17 SER B 36 ALA B 120 ALA B 121 GLY B 122 SITE 2 AC4 17 TYR B 188 GLU B 189 VAL B 205 GLY B 206 SITE 3 AC4 17 MET B 207 THR B 230 ASN B 231 LEU B 241 SITE 4 AC4 17 HIS B 243 VAL B 246 HOH B 293 HOH B 299 SITE 5 AC4 17 SO4 B 302 CRYST1 113.480 113.480 85.011 90.00 90.00 120.00 H 3 18 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 0.008812 0.005088 0.000000 0.00000 SCALE2 0.000000 0.010175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011763 0.00000