HEADER HYDROLASE/RNA/DNA 08-AUG-16 5SWM TITLE BACILLUS HALODURANS RNASE H MUTANT D132N IN COMPLEX WITH 12-MER TITLE 2 FRNA/DNA HYBRID COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RNASE H; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (12-MER); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (12-MER); COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 86665; SOURCE 4 GENE: RNHA; SOURCE 5 EXPRESSION_SYSTEM: BACILLUS HALODURANS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 86665; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 PLYSS; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS RNASE H, RNA/DNA HYBRID, HYDROLASE-RNA-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.S.PALLAN,M.EGLI REVDAT 5 04-OCT-23 5SWM 1 REMARK REVDAT 4 25-DEC-19 5SWM 1 REMARK REVDAT 3 27-SEP-17 5SWM 1 JRNL REMARK REVDAT 2 12-OCT-16 5SWM 1 JRNL REVDAT 1 21-SEP-16 5SWM 0 JRNL AUTH P.S.PALLAN,T.P.PRAKASH,A.R.DE LEON,M.EGLI JRNL TITL LIMITS OF RNA 2'-OH MIMICRY BY FLUORINE: CRYSTAL STRUCTURE JRNL TITL 2 OF BACILLUS HALODURANS RNASE H BOUND TO A 2'-FRNA:DNA JRNL TITL 3 HYBRID. JRNL REF BIOCHEMISTRY V. 55 5321 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 27611889 JRNL DOI 10.1021/ACS.BIOCHEM.6B00849 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0151 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 52981 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2680 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) : 2985 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.1530 REMARK 3 BIN FREE R VALUE SET COUNT : 140 REMARK 3 BIN FREE R VALUE : 0.1830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2133 REMARK 3 NUCLEIC ACID ATOMS : 495 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 275 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.77000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -1.12000 REMARK 3 B12 (A**2) : -0.16000 REMARK 3 B13 (A**2) : -0.04000 REMARK 3 B23 (A**2) : 0.18000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.078 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.194 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3853 ; 0.023 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 2855 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5531 ; 2.058 ; 1.995 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6663 ; 0.990 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 262 ; 6.721 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 97 ;34.168 ;24.845 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 396 ;14.266 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;20.438 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 578 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3197 ; 0.023 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 785 ; 0.003 ; 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): 1054 ; 1.315 ; 1.002 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1053 ; 1.306 ; 0.999 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1314 ; 1.935 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1315 ; 1.935 ; 1.503 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2799 ; 2.075 ; 1.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2799 ; 2.075 ; 1.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4218 ; 2.974 ; 1.437 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4645 ; 5.873 ;11.565 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4646 ; 5.876 ;11.569 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 63 A 193 REMARK 3 ORIGIN FOR THE GROUP (A): 0.4490 -0.3179 -0.4155 REMARK 3 T TENSOR REMARK 3 T11: 0.0133 T22: 0.0147 REMARK 3 T33: 0.0195 T12: 0.0108 REMARK 3 T13: -0.0039 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 0.7533 L22: 1.6139 REMARK 3 L33: 2.0927 L12: -0.2272 REMARK 3 L13: -0.2258 L23: -0.4171 REMARK 3 S TENSOR REMARK 3 S11: -0.0778 S12: -0.0556 S13: 0.0062 REMARK 3 S21: -0.0263 S22: 0.0460 S23: 0.0234 REMARK 3 S31: 0.0447 S32: 0.0058 S33: 0.0318 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 62 B 194 REMARK 3 ORIGIN FOR THE GROUP (A): -18.2683 -3.9299 40.3971 REMARK 3 T TENSOR REMARK 3 T11: 0.0100 T22: 0.0082 REMARK 3 T33: 0.0131 T12: -0.0059 REMARK 3 T13: 0.0048 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.7526 L22: 1.6363 REMARK 3 L33: 2.0330 L12: 0.2455 REMARK 3 L13: 0.1976 L23: -0.3736 REMARK 3 S TENSOR REMARK 3 S11: -0.0738 S12: 0.0506 S13: -0.0134 REMARK 3 S21: 0.0286 S22: 0.0446 S23: 0.0236 REMARK 3 S31: -0.0410 S32: 0.0026 S33: 0.0292 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 12 REMARK 3 ORIGIN FOR THE GROUP (A): 2.6335 -2.0720 20.0258 REMARK 3 T TENSOR REMARK 3 T11: 0.0363 T22: 0.0934 REMARK 3 T33: 0.0536 T12: 0.0015 REMARK 3 T13: 0.0068 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.0002 L22: 0.1200 REMARK 3 L33: 0.2513 L12: -0.0017 REMARK 3 L13: -0.0052 L23: -0.0287 REMARK 3 S TENSOR REMARK 3 S11: -0.0034 S12: 0.0006 S13: -0.0009 REMARK 3 S21: 0.0324 S22: -0.0508 S23: 0.0184 REMARK 3 S31: 0.0521 S32: -0.0051 S33: 0.0543 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 12 REMARK 3 ORIGIN FOR THE GROUP (A): 4.2083 -2.1070 20.0217 REMARK 3 T TENSOR REMARK 3 T11: 0.0547 T22: 0.1417 REMARK 3 T33: 0.0831 T12: 0.0044 REMARK 3 T13: 0.0054 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 0.0004 L22: 0.0025 REMARK 3 L33: 0.0926 L12: 0.0009 REMARK 3 L13: 0.0029 L23: 0.0109 REMARK 3 S TENSOR REMARK 3 S11: 0.0068 S12: 0.0004 S13: 0.0001 REMARK 3 S21: 0.0103 S22: 0.0072 S23: -0.0042 REMARK 3 S31: 0.0307 S32: 0.0968 S33: -0.0140 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5SWM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223084. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91836 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55661 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 26.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 46.0000 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) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.13000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.60 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: PDB ID: 1ZBI REMARK 200 REMARK 200 REMARK: CRYSTALS WITH MEDIUM THICKNESS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 M AMMONIUM PHOSPHATE MONOBASIC, REMARK 280 VAPOR DIFFUSION, 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 GLY A 55 REMARK 465 SER A 56 REMARK 465 HIS A 57 REMARK 465 MET A 58 REMARK 465 ALA A 59 REMARK 465 LYS A 60 REMARK 465 GLU A 61 REMARK 465 GLU A 62 REMARK 465 GLY A 194 REMARK 465 ARG A 195 REMARK 465 LYS A 196 REMARK 465 GLY B 55 REMARK 465 SER B 56 REMARK 465 HIS B 57 REMARK 465 MET B 58 REMARK 465 ALA B 59 REMARK 465 LYS B 60 REMARK 465 GLU B 61 REMARK 465 ARG B 195 REMARK 465 LYS B 196 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 GLU A 122 CD OE1 OE2 REMARK 470 GLU A 154 CG CD OE1 OE2 REMARK 470 GLU B 153 CD OE1 OE2 REMARK 470 GLU B 175 CG CD OE1 OE2 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 A 370 O HOH A 380 1.98 REMARK 500 OP2 UFT C 7 O HOH C 101 2.08 REMARK 500 OD2 ASP B 192 O HOH B 201 2.10 REMARK 500 OP2 DG D 10 O HOH D 201 2.14 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 66 CD GLU A 66 OE2 -0.096 REMARK 500 ASP A 71 CB ASP A 71 CG 0.132 REMARK 500 GLU A 98 CD GLU A 98 OE2 -0.085 REMARK 500 GLU A 109 CD GLU A 109 OE2 0.073 REMARK 500 TYR A 119 CG TYR A 119 CD2 -0.078 REMARK 500 GLU B 98 CD GLU B 98 OE1 -0.100 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 LYS B 146 55.03 -91.57 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 GLU A 98 0.09 SIDE CHAIN REMARK 500 ASP B 87 0.07 SIDE CHAIN REMARK 500 GLU B 98 0.08 SIDE CHAIN REMARK 500 DG D 1 0.06 SIDE CHAIN REMARK 500 DA D 3 0.06 SIDE CHAIN REMARK 500 DG D 8 0.06 SIDE CHAIN REMARK 500 DG D 10 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 399 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH B 310 DISTANCE = 6.23 ANGSTROMS 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 NA A 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 132 OD1 REMARK 620 2 THR A 183 OG1 106.9 REMARK 620 3 HOH A 302 O 82.0 100.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 101 DBREF 5SWM A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 5SWM B 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 5SWM C 1 12 PDB 5SWM 5SWM 1 12 DBREF 5SWM D 1 12 PDB 5SWM 5SWM 1 12 SEQADV 5SWM GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 5SWM SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 5SWM HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 5SWM MET A 58 UNP Q9KEI9 EXPRESSION TAG SEQADV 5SWM ASN A 132 UNP Q9KEI9 ASP 132 ENGINEERED MUTATION SEQADV 5SWM GLY B 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 5SWM SER B 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 5SWM HIS B 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 5SWM MET B 58 UNP Q9KEI9 EXPRESSION TAG SEQADV 5SWM ASN B 132 UNP Q9KEI9 ASP 132 ENGINEERED MUTATION SEQRES 1 A 142 GLY SER HIS MET ALA LYS GLU GLU ILE ILE TRP GLU SER SEQRES 2 A 142 LEU SER VAL ASP VAL GLY SER GLN GLY ASN PRO GLY ILE SEQRES 3 A 142 VAL GLU TYR LYS GLY VAL ASP THR LYS THR GLY GLU VAL SEQRES 4 A 142 LEU PHE GLU ARG GLU PRO ILE PRO ILE GLY THR ASN ASN SEQRES 5 A 142 MET GLY GLU PHE LEU ALA ILE VAL HIS GLY LEU ARG TYR SEQRES 6 A 142 LEU LYS GLU ARG ASN SER ARG LYS PRO ILE TYR SER ASN SEQRES 7 A 142 SER GLN THR ALA ILE LYS TRP VAL LYS ASP LYS LYS ALA SEQRES 8 A 142 LYS SER THR LEU VAL ARG ASN GLU GLU THR ALA LEU ILE SEQRES 9 A 142 TRP LYS LEU VAL ASP GLU ALA GLU GLU TRP LEU ASN THR SEQRES 10 A 142 HIS THR TYR GLU THR PRO ILE LEU LYS TRP GLN THR ASP SEQRES 11 A 142 LYS TRP GLY GLU ILE LYS ALA ASP TYR GLY ARG LYS SEQRES 1 B 142 GLY SER HIS MET ALA LYS GLU GLU ILE ILE TRP GLU SER SEQRES 2 B 142 LEU SER VAL ASP VAL GLY SER GLN GLY ASN PRO GLY ILE SEQRES 3 B 142 VAL GLU TYR LYS GLY VAL ASP THR LYS THR GLY GLU VAL SEQRES 4 B 142 LEU PHE GLU ARG GLU PRO ILE PRO ILE GLY THR ASN ASN SEQRES 5 B 142 MET GLY GLU PHE LEU ALA ILE VAL HIS GLY LEU ARG TYR SEQRES 6 B 142 LEU LYS GLU ARG ASN SER ARG LYS PRO ILE TYR SER ASN SEQRES 7 B 142 SER GLN THR ALA ILE LYS TRP VAL LYS ASP LYS LYS ALA SEQRES 8 B 142 LYS SER THR LEU VAL ARG ASN GLU GLU THR ALA LEU ILE SEQRES 9 B 142 TRP LYS LEU VAL ASP GLU ALA GLU GLU TRP LEU ASN THR SEQRES 10 B 142 HIS THR TYR GLU THR PRO ILE LEU LYS TRP GLN THR ASP SEQRES 11 B 142 LYS TRP GLY GLU ILE LYS ALA ASP TYR GLY ARG LYS SEQRES 1 C 12 GF2 AF2 CFZ AF2 CFZ CFZ UFT GF2 AF2 UFT UFT CFZ SEQRES 1 D 12 DG DA DA BRU DC DA DG DG DT DG DT DC HET GF2 C 1 60 HET AF2 C 2 66 HET CFZ C 3 60 HET AF2 C 4 66 HET CFZ C 5 60 HET CFZ C 6 60 HET UFT C 7 60 HET GF2 C 8 69 HET AF2 C 9 66 HET UFT C 10 60 HET UFT C 11 60 HET CFZ C 12 60 HET BRU D 4 60 HET NA A 201 1 HET CL A 202 1 HET PEG A 203 7 HET GOL D 101 6 HETNAM GF2 2'-DEOXY-2'-FLUOROGUANOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM AF2 2'-DEOXY-2'-FLUOROADENOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM CFZ 2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM UFT 2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GF2 2(C10 H13 F N5 O7 P) FORMUL 3 AF2 3(C10 H13 F N5 O6 P) FORMUL 3 CFZ 4(C9 H13 F N3 O7 P) FORMUL 3 UFT 3(C9 H12 F N2 O8 P) FORMUL 4 BRU C9 H12 BR N2 O8 P FORMUL 5 NA NA 1+ FORMUL 6 CL CL 1- FORMUL 7 PEG C4 H10 O3 FORMUL 8 GOL C3 H8 O3 FORMUL 9 HOH *275(H2 O) HELIX 1 AA1 THR A 104 ARG A 123 1 20 HELIX 2 AA2 SER A 133 LYS A 143 1 11 HELIX 3 AA3 THR A 155 ASN A 170 1 16 HELIX 4 AA4 GLN A 182 GLY A 187 1 6 HELIX 5 AA5 THR B 104 ARG B 123 1 20 HELIX 6 AA6 SER B 133 LYS B 143 1 11 HELIX 7 AA7 THR B 155 ASN B 170 1 16 HELIX 8 AA8 GLN B 182 GLY B 187 1 6 SHEET 1 AA1 3 VAL A 93 GLU A 96 0 SHEET 2 AA1 3 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA1 3 ILE A 100 GLY A 103 -1 O ILE A 100 N VAL A 81 SHEET 1 AA2 5 VAL A 93 GLU A 96 0 SHEET 2 AA2 5 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA2 5 LEU A 68 GLN A 75 -1 N SER A 69 O VAL A 86 SHEET 4 AA2 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 AA2 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 SHEET 1 AA3 3 VAL B 93 GLU B 96 0 SHEET 2 AA3 3 GLY B 79 ASP B 87 -1 N GLY B 85 O LEU B 94 SHEET 3 AA3 3 ILE B 100 GLY B 103 -1 O ILE B 100 N VAL B 81 SHEET 1 AA4 5 VAL B 93 GLU B 96 0 SHEET 2 AA4 5 GLY B 79 ASP B 87 -1 N GLY B 85 O LEU B 94 SHEET 3 AA4 5 LEU B 68 GLN B 75 -1 N SER B 69 O VAL B 86 SHEET 4 AA4 5 ILE B 129 SER B 131 1 O TYR B 130 N LEU B 68 SHEET 5 AA4 5 ILE B 178 LYS B 180 1 O LEU B 179 N ILE B 129 LINK O3'AGF2 C 1 P AAF2 C 2 1555 1555 1.63 LINK O3'BGF2 C 1 P BAF2 C 2 1555 1555 1.66 LINK O3'CGF2 C 1 P CAF2 C 2 1555 1555 1.63 LINK O3'AAF2 C 2 P ACFZ C 3 1555 1555 1.64 LINK O3'BAF2 C 2 P BCFZ C 3 1555 1555 1.66 LINK O3'CAF2 C 2 P CCFZ C 3 1555 1555 1.61 LINK O3'ACFZ C 3 P AAF2 C 4 1555 1555 1.61 LINK O3'BCFZ C 3 P BAF2 C 4 1555 1555 1.60 LINK O3'CCFZ C 3 P CAF2 C 4 1555 1555 1.57 LINK O3'AAF2 C 4 P ACFZ C 5 1555 1555 1.60 LINK O3'BAF2 C 4 P BCFZ C 5 1555 1555 1.56 LINK O3'CAF2 C 4 P CCFZ C 5 1555 1555 1.59 LINK O3'ACFZ C 5 P ACFZ C 6 1555 1555 1.60 LINK O3'BCFZ C 5 P BCFZ C 6 1555 1555 1.58 LINK O3'CCFZ C 5 P CCFZ C 6 1555 1555 1.59 LINK O3'ACFZ C 6 P AUFT C 7 1555 1555 1.59 LINK O3'BCFZ C 6 P BUFT C 7 1555 1555 1.61 LINK O3'CCFZ C 6 P CUFT C 7 1555 1555 1.61 LINK O3'AUFT C 7 P AGF2 C 8 1555 1555 1.59 LINK O3'BUFT C 7 P BGF2 C 8 1555 1555 1.62 LINK O3'CUFT C 7 P CGF2 C 8 1555 1555 1.65 LINK O3'AGF2 C 8 P AAF2 C 9 1555 1555 1.59 LINK O3'BGF2 C 8 P BAF2 C 9 1555 1555 1.62 LINK O3'CGF2 C 8 P CAF2 C 9 1555 1555 1.60 LINK O3'AAF2 C 9 P AUFT C 10 1555 1555 1.60 LINK O3'BAF2 C 9 P BUFT C 10 1555 1555 1.61 LINK O3'CAF2 C 9 P CUFT C 10 1555 1555 1.58 LINK O3'AUFT C 10 P AUFT C 11 1555 1555 1.65 LINK O3'BUFT C 10 P BUFT C 11 1555 1555 1.65 LINK O3'CUFT C 10 P CUFT C 11 1555 1555 1.57 LINK O3'AUFT C 11 P ACFZ C 12 1555 1555 1.66 LINK O3'BUFT C 11 P BCFZ C 12 1555 1555 1.65 LINK O3'CUFT C 11 P CCFZ C 12 1555 1555 1.65 LINK O3'A DA D 3 P ABRU D 4 1555 1555 1.61 LINK O3'B DA D 3 P BBRU D 4 1555 1555 1.58 LINK O3'C DA D 3 P CBRU D 4 1555 1555 1.61 LINK O3'ABRU D 4 P A DC D 5 1555 1555 1.64 LINK O3'BBRU D 4 P B DC D 5 1555 1555 1.60 LINK O3'CBRU D 4 P C DC D 5 1555 1555 1.61 LINK OD1 ASN A 132 NA NA A 201 1555 1555 3.05 LINK OG1 THR A 183 NA NA A 201 1555 1555 2.82 LINK NA NA A 201 O HOH A 302 1555 1555 2.85 CISPEP 1 ASN A 77 PRO A 78 0 2.24 CISPEP 2 ASN B 77 PRO B 78 0 5.53 SITE 1 AC1 5 ASN A 132 THR A 183 GLU A 188 ILE A 189 SITE 2 AC1 5 HOH A 302 SITE 1 AC2 5 LEU A 117 LYS A 121 TYR A 174 THR A 176 SITE 2 AC2 5 HOH A 384 SITE 1 AC3 7 TYR A 83 ARG A 97 LEU A 111 HIS A 115 SITE 2 AC3 7 HOH A 337 HOH A 373 ASN B 170 SITE 1 AC4 13 GLY B 76 ASN B 77 GF2 C 1 AF2 C 2 SITE 2 AC4 13 UFT C 7 GF2 C 8 CFZ C 12 DG D 1 SITE 3 AC4 13 DA D 2 DA D 3 DG D 7 DG D 8 SITE 4 AC4 13 HOH D 221 CRYST1 37.474 44.500 62.174 84.42 89.90 65.10 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 0.026685 -0.012386 0.001277 0.00000 SCALE2 0.000000 0.024774 -0.002652 0.00000 SCALE3 0.000000 0.000000 0.016176 0.00000