HEADER HYDROLASE/DNA 02-NOV-12 4HUE TITLE STRUCTURE OF 5-CHLOROURACIL MODIFIED G:U BASE PAIR 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: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3'); COMPND 10 CHAIN: C, D, E, F; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DICKERSON DODECAMER DNA, CLU9 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 272558; SOURCE 4 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 5 GENE: RNHA, BH0863; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS 5-CHLORO-2'-DEOXYURIDINE, W-C BASE PAIR, WOBBLE BASE PAIR, DOUBLE KEYWDS 2 HELIX, WOBBLE BASE PAIRING PATTERN, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PATRA,M.EGLI REVDAT 4 20-SEP-23 4HUE 1 REMARK SEQADV LINK REVDAT 3 27-MAR-13 4HUE 1 JRNL REVDAT 2 13-FEB-13 4HUE 1 JRNL REVDAT 1 19-DEC-12 4HUE 0 JRNL AUTH A.PATRA,J.HARP,P.S.PALLAN,L.ZHAO,M.ABRAMOV,P.HERDEWIJN, JRNL AUTH 2 M.EGLI JRNL TITL STRUCTURE, STABILITY AND FUNCTION OF 5-CHLOROURACIL MODIFIED JRNL TITL 2 A:U AND G:U BASE PAIRS. JRNL REF NUCLEIC ACIDS RES. V. 41 2689 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23275540 JRNL DOI 10.1093/NAR/GKS1316 REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 68154 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 3453 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.2827 - 4.5593 0.91 2604 149 0.2039 0.2345 REMARK 3 2 4.5593 - 3.6203 0.97 2629 149 0.1606 0.1949 REMARK 3 3 3.6203 - 3.1630 0.97 2650 140 0.1749 0.2016 REMARK 3 4 3.1630 - 2.8740 0.98 2653 142 0.1932 0.2189 REMARK 3 5 2.8740 - 2.6681 0.99 2603 161 0.1949 0.2138 REMARK 3 6 2.6681 - 2.5109 0.99 2661 131 0.1960 0.2313 REMARK 3 7 2.5109 - 2.3852 0.99 2618 139 0.1937 0.2249 REMARK 3 8 2.3852 - 2.2814 0.98 2628 137 0.1876 0.2146 REMARK 3 9 2.2814 - 2.1935 0.98 2627 146 0.1800 0.2139 REMARK 3 10 2.1935 - 2.1179 0.98 2596 130 0.1925 0.1801 REMARK 3 11 2.1179 - 2.0517 0.98 2591 161 0.1852 0.2154 REMARK 3 12 2.0517 - 1.9930 0.98 2606 141 0.1934 0.2394 REMARK 3 13 1.9930 - 1.9406 0.98 2584 154 0.1989 0.2189 REMARK 3 14 1.9406 - 1.8932 0.98 2592 121 0.1974 0.2143 REMARK 3 15 1.8932 - 1.8502 0.97 2596 105 0.2027 0.2597 REMARK 3 16 1.8502 - 1.8108 0.98 2614 114 0.2046 0.2257 REMARK 3 17 1.8108 - 1.7746 0.98 2583 139 0.2130 0.2396 REMARK 3 18 1.7746 - 1.7411 0.98 2561 133 0.2148 0.2631 REMARK 3 19 1.7411 - 1.7100 0.97 2553 138 0.2161 0.2372 REMARK 3 20 1.7100 - 1.6810 0.97 2570 124 0.2281 0.2574 REMARK 3 21 1.6810 - 1.6539 0.97 2526 145 0.2297 0.2866 REMARK 3 22 1.6539 - 1.6285 0.96 2519 135 0.2367 0.2380 REMARK 3 23 1.6285 - 1.6045 0.97 2522 157 0.2491 0.3002 REMARK 3 24 1.6045 - 1.5819 0.97 2535 145 0.2450 0.3073 REMARK 3 25 1.5819 - 1.5605 0.94 2480 117 0.2701 0.2440 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3201 REMARK 3 ANGLE : 1.229 4520 REMARK 3 CHIRALITY : 0.069 488 REMARK 3 PLANARITY : 0.005 429 REMARK 3 DIHEDRAL : 23.016 1249 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4HUE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000075932. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.97930 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68193 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: 3D0P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM REMARK 280 CACODYLATE AND 20% (W/V) PEG 8000, PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K 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 32.18000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.31100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.40400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.31100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.18000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.40400 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, F 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 UCL E 9 REMARK 465 DG E 10 REMARK 465 DC E 11 REMARK 465 DG E 12 REMARK 465 DC F 13 REMARK 465 DG F 14 REMARK 465 DC F 15 REMARK 465 DG F 16 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 ARG A 126 NE CZ NH1 NH2 REMARK 470 GLU A 175 CD OE1 OE2 REMARK 470 GLU B 122 CD OE1 OE2 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 ARG A 118 CA CB CG CD NE CZ NH1 REMARK 480 ARG A 118 NH2 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 O1 GOL E 101 O HOH E 216 1.97 REMARK 500 O2 GOL E 101 O HOH E 217 2.07 REMARK 500 OE2 GLU B 175 O HOH B 311 2.09 REMARK 500 O HOH A 441 O HOH A 457 2.14 REMARK 500 O HOH A 407 O HOH A 440 2.14 REMARK 500 O HOH A 413 O HOH A 420 2.17 REMARK 500 O HOH A 410 O HOH C 117 2.18 REMARK 500 O HOH A 335 O HOH A 413 2.18 REMARK 500 O HOH A 396 O HOH A 415 2.19 REMARK 500 O HOH B 272 O HOH B 319 2.19 REMARK 500 OE1 GLU B 92 O HOH B 323 2.19 REMARK 500 OE1 GLU B 154 O HOH B 304 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 188 O HOH A 438 4455 2.19 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 DC C 3 C6 - N1 - C2 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT C 8 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG C 10 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DC C 11 C3' - C2' - C1' ANGL. DEV. = -6.7 DEGREES REMARK 500 DG C 12 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DG C 12 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG D 14 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DC D 15 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 DC D 15 O4' - C1' - N1 ANGL. DEV. = 7.7 DEGREES REMARK 500 DG D 24 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT E 7 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA F 17 O4' - C4' - C3' ANGL. DEV. = -6.9 DEGREES REMARK 500 DA F 17 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 DG F 22 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG F 22 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES 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 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE2 85.4 REMARK 620 3 HOH A 340 O 90.8 171.5 REMARK 620 4 HOH A 349 O 96.5 105.6 82.4 REMARK 620 5 HOH A 383 O 171.9 96.2 86.6 90.7 REMARK 620 6 HOH A 445 O 104.5 76.8 96.8 159.1 68.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG E 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG E 2 OP2 REMARK 620 2 HOH E 210 O 94.2 REMARK 620 3 HOH E 211 O 85.7 176.8 REMARK 620 4 HOH E 213 O 88.2 91.1 92.1 REMARK 620 5 HOH E 214 O 168.1 96.7 83.6 86.9 REMARK 620 6 HOH E 216 O 94.4 83.1 93.7 173.8 91.6 REMARK 620 N 1 2 3 4 5 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HTU RELATED DB: PDB REMARK 900 STRUCTURE OF 5-CHLOROURACIL MODIFIED A:U BASE PAIR REMARK 900 RELATED ID: 4HUF RELATED DB: PDB REMARK 900 RELATED ID: 4HUG RELATED DB: PDB DBREF 4HUE A 61 194 UNP Q9KEI9 RNH1_BACHD 61 194 DBREF 4HUE B 61 194 UNP Q9KEI9 RNH1_BACHD 61 194 DBREF 4HUE C 1 12 PDB 4HUE 4HUE 1 12 DBREF 4HUE D 13 24 PDB 4HUE 4HUE 13 24 DBREF 4HUE E 1 12 PDB 4HUE 4HUE 1 12 DBREF 4HUE F 13 24 PDB 4HUE 4HUE 13 24 SEQADV 4HUE ASN A 132 UNP Q9KEI9 ASP 132 ENGINEERED MUTATION SEQADV 4HUE ASN B 132 UNP Q9KEI9 ASP 132 ENGINEERED MUTATION SEQRES 1 A 134 GLU GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SEQRES 2 A 134 SER GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL SEQRES 3 A 134 ASP THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO SEQRES 4 A 134 ILE PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA SEQRES 5 A 134 ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER SEQRES 6 A 134 ARG LYS PRO ILE TYR SER ASN SER GLN THR ALA ILE LYS SEQRES 7 A 134 TRP VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG SEQRES 8 A 134 ASN GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU SEQRES 9 A 134 ALA GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO SEQRES 10 A 134 ILE LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS SEQRES 11 A 134 ALA ASP TYR GLY SEQRES 1 B 134 GLU GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SEQRES 2 B 134 SER GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL SEQRES 3 B 134 ASP THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO SEQRES 4 B 134 ILE PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA SEQRES 5 B 134 ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER SEQRES 6 B 134 ARG LYS PRO ILE TYR SER ASN SER GLN THR ALA ILE LYS SEQRES 7 B 134 TRP VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG SEQRES 8 B 134 ASN GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU SEQRES 9 B 134 ALA GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO SEQRES 10 B 134 ILE LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS SEQRES 11 B 134 ALA ASP TYR GLY SEQRES 1 C 12 DC DG DC DG DA DA DT DT UCL DG DC DG SEQRES 1 D 12 DC DG DC DG DA DA DT DT UCL DG DC DG SEQRES 1 E 12 DC DG DC DG DA DA DT DT UCL DG DC DG SEQRES 1 F 12 DC DG DC DG DA DA DT DT UCL DG DC DG MODRES 4HUE UCL C 9 DU MODRES 4HUE UCL D 21 DU MODRES 4HUE UCL F 21 DU HET UCL C 9 20 HET UCL D 21 20 HET UCL F 21 20 HET GOL A 201 6 HET GOL A 202 6 HET MG A 203 1 HET GOL D 101 6 HET GOL E 101 6 HET MG E 102 1 HETNAM UCL 5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 UCL 3(C9 H12 CL N2 O8 P) FORMUL 7 GOL 4(C3 H8 O3) FORMUL 9 MG 2(MG 2+) FORMUL 13 HOH *457(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 B 104 ASN B 124 1 21 HELIX 6 6 SER B 133 LYS B 143 1 11 HELIX 7 7 THR B 155 HIS B 172 1 18 HELIX 8 8 GLN B 182 GLY B 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 GLN A 75 -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 B 93 GLY B 103 0 SHEET 2 B 5 GLY B 79 ASP B 87 -1 N VAL B 81 O ILE B 100 SHEET 3 B 5 LEU B 68 GLN B 75 -1 N SER B 69 O VAL B 86 SHEET 4 B 5 ILE B 129 SER B 131 1 O TYR B 130 N LEU B 68 SHEET 5 B 5 ILE B 178 LYS B 180 1 O LEU B 179 N ILE B 129 LINK O3' DT C 8 P UCL C 9 1555 1555 1.61 LINK O3' DT D 20 P UCL D 21 1555 1555 1.61 LINK O3' DT F 20 P UCL F 21 1555 1555 1.61 LINK OD1 ASP A 71 MG MG A 203 1555 1555 2.34 LINK OE2 GLU A 109 MG MG A 203 1555 1555 1.99 LINK MG MG A 203 O HOH A 340 1555 1555 2.05 LINK MG MG A 203 O HOH A 349 1555 1555 2.09 LINK MG MG A 203 O HOH A 383 1555 1555 2.07 LINK MG MG A 203 O HOH A 445 1555 1555 2.05 LINK OP2 DG E 2 MG MG E 102 1555 1555 2.01 LINK MG MG E 102 O HOH E 210 1555 1555 2.05 LINK MG MG E 102 O HOH E 211 1555 1555 2.08 LINK MG MG E 102 O HOH E 213 1555 1555 2.09 LINK MG MG E 102 O HOH E 214 1555 1555 2.06 LINK MG MG E 102 O HOH E 216 1555 1555 2.06 CISPEP 1 ASN A 77 PRO A 78 0 -3.36 CISPEP 2 ASN B 77 PRO B 78 0 3.92 SITE 1 AC1 9 GLY A 76 ASN A 77 PRO A 78 HOH A 357 SITE 2 AC1 9 HOH A 407 HOH A 417 THR B 176 PRO B 177 SITE 3 AC1 9 ILE B 178 SITE 1 AC2 8 LYS A 143 THR A 173 TYR A 174 HOH A 423 SITE 2 AC2 8 DC F 23 DG F 24 HOH F 103 HOH F 107 SITE 1 AC3 7 ASP A 71 GLU A 109 ASN A 132 HOH A 340 SITE 2 AC3 7 HOH A 349 HOH A 383 HOH A 445 SITE 1 AC4 11 THR A 135 DG C 2 HOH C 127 DG D 22 SITE 2 AC4 11 DC D 23 DG D 24 HOH D 201 HOH D 203 SITE 3 AC4 11 HOH D 204 HOH D 208 HOH D 220 SITE 1 AC5 12 LYS A 141 ASP A 142 DG E 2 DC E 3 SITE 2 AC5 12 MG E 102 HOH E 215 HOH E 216 HOH E 217 SITE 3 AC5 12 HOH E 219 UCL F 21 DG F 22 HOH F 119 SITE 1 AC6 7 DG E 2 GOL E 101 HOH E 210 HOH E 211 SITE 2 AC6 7 HOH E 213 HOH E 214 HOH E 216 CRYST1 64.360 64.808 116.622 90.00 90.00 90.00 P 21 21 21 16 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 0.015538 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015430 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008575 0.00000