HEADER DNA/RNA 05-APR-01 1IDW TITLE STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[CL]U IN PRESENCE OF TITLE 2 RH(NH3)6+++ COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UCL))-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: PHOSPHORAMIDITE METHOD KEYWDS RNA/DNA HYBRID, RHODIUM HEXAMMINE, C-U MISMATCH, G-U MISMATCH, DNA- KEYWDS 2 RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.CRUSE,P.SALUDJIAN,A.NEUMAN,T.PRANGE REVDAT 7 09-AUG-23 1IDW 1 REMARK LINK REVDAT 6 18-APR-18 1IDW 1 REMARK REVDAT 5 04-OCT-17 1IDW 1 REMARK REVDAT 4 24-FEB-09 1IDW 1 VERSN REVDAT 3 01-APR-03 1IDW 1 JRNL REVDAT 2 02-NOV-01 1IDW 1 JRNL REVDAT 1 12-APR-01 1IDW 0 JRNL AUTH W.CRUSE,P.SALUDJIAN,A.NEUMAN,T.PRANGE JRNL TITL DESTABILIZING EFFECT OF A FLUOROURACIL EXTRA BASE IN A JRNL TITL 2 HYBRID RNA DUPLEX COMPARED WITH BROMO AND CHLORO ANALOGUES JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 1609 2001 JRNL REFN ISSN 0907-4449 JRNL PMID 11679725 JRNL DOI 10.1107/S0907444901012318 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.CRUSE,P.SALUDJIAN,E.BIALA,P.STRAZEWSKI,T.PRANGE,O.KENNARD REMARK 1 TITL STRUCTURE OF A MISPAIRED RNA DOUBLE HELIX AT 1.6 A REMARK 1 TITL 2 RESOLUTION AND IMPLICATIONS FOR THE PREDICTION OF RNA REMARK 1 TITL 3 SECONDARY STRUCTURE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 91 4160 1994 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.176 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.172 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 311 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 3738 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 372 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 46 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.071 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.097 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : PERSONAL DICTIONARY FROM SMALL REMARK 3 MOLECULES REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 CHLORO-URACIL 9 B DISORDERED AT THE C2 POSITION. REMARK 3 REFINED AS TWO-COMPONENT 1:1 STATIC ORIENTATIONS REMARK 3 PAIRED TO THEIR SYMMETRY-RELATED MATES. REMARK 3 THE TWO RHODIUM ATOMS ARE REFINED ANISOTROPICALLY. REMARK 3 ONE CHLORINE ATOM IS DISORDERED. REMARK 4 REMARK 4 1IDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013190. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-97 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS FAST REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ROTAVATA, MADNESS REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, ROTAVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3641 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 6.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : 0.04100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 43.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.21200 REMARK 200 R SYM FOR SHELL (I) : 0.20600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 165D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CACODYLATE BUFFER, MPD, RHODIUM REMARK 280 -HEXAMMINE, PH 6.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K 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 26.91000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 9.69000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.91000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 9.69000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE SECOND STRAND OF THE DIMER IS NOT SYMMETRIC REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 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 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 G A 1 C6 - N1 - C2 ANGL. DEV. = -3.6 DEGREES REMARK 500 U A 3 N1 - C2 - N3 ANGL. DEV. = 4.2 DEGREES REMARK 500 U A 3 C2 - N3 - C4 ANGL. DEV. = -4.7 DEGREES REMARK 500 U A 3 C5 - C4 - O4 ANGL. DEV. = -3.9 DEGREES REMARK 500 U A 4 C5 - C4 - O4 ANGL. DEV. = -4.9 DEGREES REMARK 500 C A 5 N3 - C4 - C5 ANGL. DEV. = -2.4 DEGREES REMARK 500 G A 6 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 G A 7 O5' - C5' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 G B 1 C6 - N1 - C2 ANGL. DEV. = -4.8 DEGREES REMARK 500 G B 1 N1 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 U B 3 C5 - C4 - O4 ANGL. DEV. = -4.3 DEGREES REMARK 500 U B 4 C2 - N3 - C4 ANGL. DEV. = -4.2 DEGREES REMARK 500 G B 6 O5' - C5' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 C B 8 O4' - C1' - N1 ANGL. DEV. = -6.4 DEGREES REMARK 500 C B 8 C3' - O3' - P ANGL. DEV. = -12.4 DEGREES REMARK 500 C B 8 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 UCL B 9 O3' - P - O5' ANGL. DEV. = 17.7 DEGREES REMARK 500 UCL B 9 O3' - P - O5' ANGL. DEV. = 12.8 DEGREES 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 RHD A 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RHD A 12 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ICG RELATED DB: PDB REMARK 900 A FLUORO-URACIL REPLACES THE CHLORO-URACIL AT POSITION #9 DBREF 1IDW A 1 9 PDB 1IDW 1IDW 1 9 DBREF 1IDW B 1 9 PDB 1IDW 1IDW 1 9 SEQRES 1 A 9 G C U U C G G C UCL SEQRES 1 B 9 G C U U C G G C UCL MODRES 1IDW UCL A 9 DU MODRES 1IDW UCL B 9 DU HET UCL A 9 20 HET UCL B 9 40 HET RHD A 11 7 HET RHD A 12 7 HET CL A 32 1 HET CL B 31 2 HETNAM UCL 5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM RHD RHODIUM HEXAMINE ION HETNAM CL CHLORIDE ION FORMUL 1 UCL 2(C9 H12 CL N2 O8 P) FORMUL 3 RHD 2(H18 N6 RH 3+) FORMUL 5 CL 2(CL 1-) FORMUL 7 HOH *46(H2 O) LINK O3' C A 8 P UCL A 9 1555 1555 1.59 LINK O3' C B 8 P AUCL B 9 1555 1555 1.59 LINK O3' C B 8 P BUCL B 9 1555 1555 1.56 SITE 1 AC1 4 C A 5 G A 6 G A 7 HOH A 106 SITE 1 AC2 5 C A 5 G A 7 C A 8 C B 5 SITE 2 AC2 5 HOH B 126 CRYST1 53.820 19.380 50.300 90.00 109.90 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 0.018580 0.000000 0.006726 0.00000 SCALE2 0.000000 0.051600 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021143 0.00000