HEADER HYDROLASE/DNA 09-JUL-09 3I8D TITLE THE PAIRING GEOMETRY OF THE HYDROPHOBIC THYMINE ANALOG 2,4- TITLE 2 DIFLUOROTOLUENE IN DUPLEX DNA AS ANALYZED BY X-RAY CRYSTALLOGRAPHY COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: RNASE-H; COMPND 5 SYNONYM: RNASE H; COMPND 6 EC: 3.1.26.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*CP*GP*CP*GP*AP*AP*TP*(DFT)P*CP*GP*CP*G)-3'; COMPND 11 CHAIN: B, D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 86665; SOURCE 4 GENE: BACILLUS HALODURANS, BH0863, RNASE-H D132N MUTANT, RNHA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES KEYWDS RNASE-H, RNASE-H DNA-COMPLEX, 2, 4-DIFLUOROTOLUENE, THYMINE ISOSTERE, KEYWDS 2 HYDROPHOBIC BASE, ENDONUCLEASE, HYDROLASE, MAGNESIUM, MANGANESE, KEYWDS 3 METAL-BINDING, NUCLEASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.EGLI,P.S.PALLAN REVDAT 6 06-SEP-23 3I8D 1 REMARK REVDAT 5 13-OCT-21 3I8D 1 REMARK SEQADV LINK REVDAT 4 01-NOV-17 3I8D 1 REMARK REVDAT 3 13-JUL-11 3I8D 1 VERSN REVDAT 2 15-SEP-09 3I8D 1 JRNL REVDAT 1 01-SEP-09 3I8D 0 JRNL AUTH P.S.PALLAN,M.EGLI JRNL TITL PAIRING GEOMETRY OF THE HYDROPHOBIC THYMINE ANALOGUE JRNL TITL 2 2,4-DIFLUOROTOLUENE IN DUPLEX DNA AS ANALYZED BY X-RAY JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF J.AM.CHEM.SOC. V. 131 12548 2009 JRNL REFN ISSN 0002-7863 JRNL PMID 19685868 JRNL DOI 10.1021/JA905739J REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0093 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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 50108 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2690 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) : 1.61 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2922 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3290 REMARK 3 BIN FREE R VALUE SET COUNT : 158 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2154 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 231 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.58000 REMARK 3 B22 (A**2) : -0.94000 REMARK 3 B33 (A**2) : 0.82000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.69000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.088 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.099 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2745 ; 0.030 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3811 ; 2.536 ; 2.181 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 262 ; 6.241 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;32.772 ;25.306 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 395 ;14.637 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;14.398 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 416 ; 0.185 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1892 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1310 ; 1.457 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2127 ; 2.359 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1435 ; 3.429 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1682 ; 4.664 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 62 A 193 REMARK 3 RESIDUE RANGE : A 601 A 601 REMARK 3 RESIDUE RANGE : A 1 A 242 REMARK 3 ORIGIN FOR THE GROUP (A): 21.2488 -1.2438 2.6758 REMARK 3 T TENSOR REMARK 3 T11: 0.0566 T22: 0.1546 REMARK 3 T33: 0.0206 T12: -0.0192 REMARK 3 T13: -0.0151 T23: 0.0429 REMARK 3 L TENSOR REMARK 3 L11: 1.7461 L22: 3.7545 REMARK 3 L33: 2.1269 L12: 0.1683 REMARK 3 L13: 0.4628 L23: -0.1681 REMARK 3 S TENSOR REMARK 3 S11: 0.0484 S12: -0.0075 S13: -0.0831 REMARK 3 S21: 0.2655 S22: -0.0966 S23: -0.0531 REMARK 3 S31: -0.0371 S32: 0.4430 S33: 0.0482 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 12 REMARK 3 RESIDUE RANGE : B 13 B 218 REMARK 3 ORIGIN FOR THE GROUP (A): 1.1335 8.5868 0.0880 REMARK 3 T TENSOR REMARK 3 T11: 0.1763 T22: 0.0441 REMARK 3 T33: 0.1824 T12: -0.0010 REMARK 3 T13: -0.0466 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 3.3974 L22: 0.1289 REMARK 3 L33: 1.3937 L12: 0.6534 REMARK 3 L13: -1.0793 L23: -0.2565 REMARK 3 S TENSOR REMARK 3 S11: -0.0347 S12: 0.0206 S13: 0.2315 REMARK 3 S21: 0.0096 S22: 0.0054 S23: 0.0289 REMARK 3 S31: -0.2044 S32: 0.0117 S33: 0.0293 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 62 C 193 REMARK 3 RESIDUE RANGE : C 602 C 604 REMARK 3 RESIDUE RANGE : C 14 C 258 REMARK 3 ORIGIN FOR THE GROUP (A): 49.5375 2.3524 36.1506 REMARK 3 T TENSOR REMARK 3 T11: 0.0310 T22: 0.0423 REMARK 3 T33: 0.0174 T12: 0.0056 REMARK 3 T13: 0.0046 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 1.4675 L22: 5.3768 REMARK 3 L33: 1.0123 L12: 0.5774 REMARK 3 L13: 0.4737 L23: -0.1155 REMARK 3 S TENSOR REMARK 3 S11: -0.0268 S12: 0.0692 S13: -0.0111 REMARK 3 S21: 0.1402 S22: 0.0680 S23: 0.1862 REMARK 3 S31: -0.0071 S32: 0.0844 S33: -0.0412 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 12 REMARK 3 RESIDUE RANGE : D 13 D 232 REMARK 3 ORIGIN FOR THE GROUP (A): 29.4547 12.2035 32.9187 REMARK 3 T TENSOR REMARK 3 T11: 0.1325 T22: 0.0680 REMARK 3 T33: 0.4513 T12: 0.0015 REMARK 3 T13: -0.0771 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 5.7599 L22: 0.1379 REMARK 3 L33: 0.4733 L12: 0.8823 REMARK 3 L13: -0.8664 L23: -0.1054 REMARK 3 S TENSOR REMARK 3 S11: -0.2099 S12: -0.0588 S13: 0.2732 REMARK 3 S21: -0.0374 S22: 0.0006 S23: 0.0557 REMARK 3 S31: 0.0369 S32: 0.0853 S33: 0.2093 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: TLS REFINEMENT IN REFMAC WAS USED REMARK 4 REMARK 4 3I8D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054092. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9787 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52821 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 39.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: USING MOLREP REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ID 3D0P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NAOAC 3H2O (PH 4.6) AND 8% (W/V) REMARK 280 PEG 4000 , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 48.08900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.35700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.08900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.35700 REMARK 290 SMTRY3 4 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE TWO FOLD AXIS ROTATION OF CHAIN A AND B BY: -X, Y, -Z. 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 -1.000000 0.000000 0.000000 56.17957 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 66.46342 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 GLN A 75 CB CG CD OE1 NE2 REMARK 480 ARG A 126 CG CD NE CZ NH1 NH2 REMARK 480 GLN C 75 CB CG CD OE1 NE2 REMARK 480 ARG C 126 CD NE CZ NH1 NH2 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 GLN A 75 N GLN A 75 CA 0.121 REMARK 500 GLN A 75 CA GLN A 75 CB -0.631 REMARK 500 ASN A 105 CB ASN A 105 CG 0.304 REMARK 500 ASN A 105 CG ASN A 105 OD1 0.167 REMARK 500 SER A 131 CB SER A 131 OG 0.078 REMARK 500 DC B 1 O3' DG B 2 P -0.086 REMARK 500 DC B 3 P DC B 3 O5' 0.073 REMARK 500 DC B 3 O3' DC B 3 C3' 0.106 REMARK 500 DC B 3 C4 DC B 3 C5 0.050 REMARK 500 DG B 4 C2' DG B 4 C1' 0.061 REMARK 500 DG B 4 C8 DG B 4 N9 0.047 REMARK 500 DA B 5 N9 DA B 5 C4 0.037 REMARK 500 DA B 6 C5' DA B 6 C4' 0.044 REMARK 500 DC B 11 O3' DC B 11 C3' -0.040 REMARK 500 DG B 12 C8 DG B 12 N9 -0.043 REMARK 500 ASP C 71 CG ASP C 71 OD2 0.144 REMARK 500 GLN C 75 CA GLN C 75 CB -0.604 REMARK 500 GLU C 153 CB GLU C 153 CG 0.116 REMARK 500 TRP C 181 CZ3 TRP C 181 CH2 0.098 REMARK 500 GLU C 188 CB GLU C 188 CG -0.201 REMARK 500 DC D 3 P DC D 3 O5' 0.093 REMARK 500 DC D 3 O3' DC D 3 C3' 0.084 REMARK 500 DG D 4 P DG D 4 O5' -0.095 REMARK 500 DG D 4 O3' DG D 4 C3' -0.059 REMARK 500 DA D 5 P DA D 5 O5' -0.069 REMARK 500 DA D 5 N3 DA D 5 C4 0.036 REMARK 500 DA D 6 C5 DA D 6 N7 -0.039 REMARK 500 DC D 9 O3' DC D 9 C3' -0.082 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 97 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 123 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 126 CA - CB - CG ANGL. DEV. = -17.2 DEGREES REMARK 500 ASP A 163 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 DC B 1 O4' - C1' - C2' ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 1 C2 - N3 - C4 ANGL. DEV. = 4.6 DEGREES REMARK 500 DC B 1 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG B 2 O3' - P - OP2 ANGL. DEV. = 9.5 DEGREES REMARK 500 DG B 2 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG B 2 C2 - N3 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 DG B 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DG B 2 N3 - C4 - N9 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC B 3 O5' - C5' - C4' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC B 3 O4' - C1' - N1 ANGL. DEV. = -6.7 DEGREES REMARK 500 DG B 4 O5' - C5' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG B 4 C2 - N3 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG B 4 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 5 C5 - N7 - C8 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA B 5 N7 - C8 - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 DA B 5 C8 - N9 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA B 5 N1 - C6 - N6 ANGL. DEV. = 5.0 DEGREES REMARK 500 DA B 6 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 DA B 6 N1 - C6 - N6 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT B 7 O5' - P - OP2 ANGL. DEV. = -6.1 DEGREES REMARK 500 DT B 7 C5 - C4 - O4 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT B 7 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 DC B 9 O4' - C4' - C3' ANGL. DEV. = -6.6 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC B 9 C2 - N3 - C4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC B 9 N3 - C4 - C5 ANGL. DEV. = -3.4 DEGREES REMARK 500 DC B 9 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 10 C6 - N1 - C2 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG B 10 N1 - C2 - N3 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG B 10 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 10 N9 - C4 - C5 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG B 10 N3 - C4 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 10 N3 - C2 - N2 ANGL. DEV. = -6.6 DEGREES REMARK 500 DC B 11 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DC B 11 C1' - O4' - C4' ANGL. DEV. = -7.5 DEGREES REMARK 500 DC B 11 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 LEU C 94 CB - CG - CD1 ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG C 97 NE - CZ - NH1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG C 151 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 GLU C 188 CB - CG - CD ANGL. DEV. = -16.4 DEGREES REMARK 500 GLU C 188 OE1 - CD - OE2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ASP C 192 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 DC D 1 O4' - C1' - C2' ANGL. DEV. = 3.6 DEGREES REMARK 500 DC D 1 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC D 1 N1 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG D 2 O4' - C4' - C3' ANGL. DEV. = 5.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 79 ANGLE DEVIATIONS. 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 SER A 74 -54.46 -128.04 REMARK 500 GLN A 75 -106.75 64.78 REMARK 500 GLN C 75 -91.78 -96.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG C 126 0.09 SIDE CHAIN 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 GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 604 DBREF 3I8D A 62 193 UNP Q9KEI9 RNH1_BACHD 62 193 DBREF 3I8D C 62 193 UNP Q9KEI9 RNH1_BACHD 62 193 DBREF 3I8D B 1 12 PDB 3I8D 3I8D 1 12 DBREF 3I8D D 1 12 PDB 3I8D 3I8D 1 12 SEQADV 3I8D ASN A 132 UNP Q9KEI9 ASP 132 ENGINEERED MUTATION SEQADV 3I8D ASN C 132 UNP Q9KEI9 ASP 132 ENGINEERED MUTATION SEQRES 1 A 132 GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SER SEQRES 2 A 132 GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL ASP SEQRES 3 A 132 THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO ILE SEQRES 4 A 132 PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA ILE SEQRES 5 A 132 VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER ARG SEQRES 6 A 132 LYS PRO ILE TYR SER ASN SER GLN THR ALA ILE LYS TRP SEQRES 7 A 132 VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG ASN SEQRES 8 A 132 GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU ALA SEQRES 9 A 132 GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO ILE SEQRES 10 A 132 LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS ALA SEQRES 11 A 132 ASP TYR SEQRES 1 B 12 DC DG DC DG DA DA DT DFT DC DG DC DG SEQRES 1 C 132 GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SER SEQRES 2 C 132 GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL ASP SEQRES 3 C 132 THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO ILE SEQRES 4 C 132 PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA ILE SEQRES 5 C 132 VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER ARG SEQRES 6 C 132 LYS PRO ILE TYR SER ASN SER GLN THR ALA ILE LYS TRP SEQRES 7 C 132 VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG ASN SEQRES 8 C 132 GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU ALA SEQRES 9 C 132 GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO ILE SEQRES 10 C 132 LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS ALA SEQRES 11 C 132 ASP TYR SEQRES 1 D 12 DC DG DC DG DA DA DT DFT DC DG DC DG HET DFT B 8 20 HET DFT D 8 20 HET GOL A 601 6 HET GOL C 602 6 HET GOL C 603 6 HET GOL C 604 6 HETNAM DFT 1-[2-DEOXYRIBOFURANOSYL]-2,4-DIFLUORO-5-METHYL-BENZENE- HETNAM 2 DFT 5'MONOPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DFT 2(C12 H15 F2 O6 P) FORMUL 5 GOL 4(C3 H8 O3) FORMUL 9 HOH *231(H2 O) HELIX 1 1 THR A 104 ARG A 123 1 20 HELIX 2 2 SER A 133 LYS A 143 1 11 HELIX 3 3 THR A 155 HIS A 172 1 18 HELIX 4 4 GLN A 182 GLY A 187 1 6 HELIX 5 5 THR C 104 ARG C 123 1 20 HELIX 6 6 SER C 133 LYS C 143 1 11 HELIX 7 7 ASN C 152 GLU C 154 5 3 HELIX 8 8 THR C 155 HIS C 172 1 18 HELIX 9 9 GLN C 182 GLY C 187 1 6 SHEET 1 A 5 VAL A 93 GLY A 103 0 SHEET 2 A 5 GLY A 79 ASP A 87 -1 N VAL A 81 O ILE A 100 SHEET 3 A 5 LEU A 68 GLY A 73 -1 N SER A 69 O VAL A 86 SHEET 4 A 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 A 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 SHEET 1 B 5 VAL C 93 GLY C 103 0 SHEET 2 B 5 GLY C 79 ASP C 87 -1 N VAL C 81 O ILE C 100 SHEET 3 B 5 LEU C 68 SER C 74 -1 N SER C 69 O VAL C 86 SHEET 4 B 5 ILE C 129 SER C 131 1 O TYR C 130 N LEU C 68 SHEET 5 B 5 ILE C 178 LYS C 180 1 O LEU C 179 N ILE C 129 LINK O3' DT B 7 P DFT B 8 1555 1555 1.64 LINK O3' DFT B 8 P DC B 9 1555 1555 1.62 LINK O3' DT D 7 P DFT D 8 1555 1555 1.66 LINK O3' DFT D 8 P DC D 9 1555 1555 1.61 CISPEP 1 ASN A 77 PRO A 78 0 10.67 CISPEP 2 ASN C 77 PRO C 78 0 2.56 SITE 1 AC1 5 HOH A 25 TYR A 83 VAL A 114 HIS A 115 SITE 2 AC1 5 ARG A 118 SITE 1 AC2 6 HIS C 115 ARG C 118 ALA C 165 HOH C 215 SITE 2 AC2 6 HOH C 243 GOL C 603 SITE 1 AC3 6 HIS C 115 TYR C 119 GLU C 122 HOH C 197 SITE 2 AC3 6 HOH C 217 GOL C 602 SITE 1 AC4 5 GLY C 73 SER C 74 GLU C 82 TYR C 193 SITE 2 AC4 5 DG D 12 CRYST1 96.178 66.714 77.571 90.00 121.04 90.00 C 1 2 1 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 0.010397 0.000000 0.006258 0.00000 SCALE2 0.000000 0.014989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015046 0.00000