HEADER DNA/RNA 04-APR-01 1ID9 TITLE STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]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*(UFP))-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, FLUORO URACIL, RHODIUM(III) HEXAMMINE, C-U MISMATCH, KEYWDS 2 G-U MISMATCH, DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.CRUSE,P.SALUDJIAN,A.NEUMAN,T.PRANGE REVDAT 5 09-AUG-23 1ID9 1 REMARK LINK REVDAT 4 24-FEB-09 1ID9 1 VERSN REVDAT 3 01-APR-03 1ID9 1 JRNL REVDAT 2 02-NOV-01 1ID9 1 JRNL REVDAT 1 12-APR-01 1ID9 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 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) : 0.155 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.153 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 410 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 4425 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 : 50 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) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.027 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.020 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.074 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 LAST FLUORO-URACIL (CHAIN B) REFINED AS A REMARK 3 TWO-POSITION DISORDER REMARK 4 REMARK 4 1ID9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013179. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW32 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.967 REMARK 200 MONOCHROMATOR : CURVATED SI(111) MIRROR REMARK 200 OPTICS : SI(111) REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4339 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 11.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : 0.04500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.14100 REMARK 200 R SYM FOR SHELL (I) : 0.16000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 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: PDB ENTRY 165D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CACODYLATE, MPD, RHODIUM(III) 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 26.86500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 9.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.86500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 9.69500 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 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 C A 2 C2 - N3 - C4 ANGL. DEV. = 4.2 DEGREES REMARK 500 C A 2 N3 - C4 - C5 ANGL. DEV. = -3.3 DEGREES REMARK 500 C A 2 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 U A 3 C2 - N3 - C4 ANGL. DEV. = -5.3 DEGREES REMARK 500 U A 3 N3 - C4 - C5 ANGL. DEV. = 4.2 DEGREES REMARK 500 U A 3 C5 - C4 - O4 ANGL. DEV. = -5.6 DEGREES REMARK 500 U A 4 O5' - C5' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 U A 4 N1 - C2 - N3 ANGL. DEV. = 3.8 DEGREES REMARK 500 U A 4 C2 - N3 - C4 ANGL. DEV. = -4.1 DEGREES REMARK 500 U A 4 C5 - C4 - O4 ANGL. DEV. = -4.8 DEGREES REMARK 500 C A 5 N3 - C4 - C5 ANGL. DEV. = -2.4 DEGREES REMARK 500 G A 6 C4 - C5 - C6 ANGL. DEV. = -4.1 DEGREES REMARK 500 G A 6 C5 - C6 - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 6 C5 - C6 - O6 ANGL. DEV. = -7.3 DEGREES REMARK 500 G A 7 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 C A 8 N3 - C4 - C5 ANGL. DEV. = -2.4 DEGREES REMARK 500 C A 8 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES REMARK 500 G B 1 C6 - N1 - C2 ANGL. DEV. = -3.9 DEGREES REMARK 500 C B 2 N3 - C4 - C5 ANGL. DEV. = -3.3 DEGREES REMARK 500 C B 2 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 U B 3 C6 - N1 - C2 ANGL. DEV. = -3.8 DEGREES REMARK 500 U B 3 N1 - C2 - N3 ANGL. DEV. = 3.9 DEGREES REMARK 500 U B 4 C2 - N3 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 U B 4 C5 - C4 - O4 ANGL. DEV. = -3.8 DEGREES REMARK 500 C B 5 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 C B 5 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 G B 6 O5' - C5' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 C B 8 N3 - C4 - C5 ANGL. DEV. = -2.6 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 RHODIUM HEXAMMINE REPLACED BY IRIDIUM HEXAMMINE DBREF 1ID9 A 1 9 PDB 1ID9 1ID9 1 9 DBREF 1ID9 B 1 9 PDB 1ID9 1ID9 1 9 SEQRES 1 A 9 G C U U C G G C UFP SEQRES 1 B 9 G C U U C G G C UFP HET UFP A 9 20 HET UFP B 9 36 HET RHD A 11 7 HET RHD A 12 7 HET CL A 32 1 HET CL B 31 1 HETNAM UFP 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM RHD RHODIUM HEXAMINE ION HETNAM CL CHLORIDE ION FORMUL 1 UFP 2(C9 H12 F N2 O8 P) FORMUL 3 RHD 2(H18 N6 RH 3+) FORMUL 5 CL 2(CL 1-) FORMUL 7 HOH *50(H2 O) LINK O3' C A 8 P UFP A 9 1555 1555 1.59 LINK O3' C B 8 P UFP B 9 1555 1555 1.62 SITE 1 AC1 5 C A 5 G A 6 G A 7 HOH A 117 SITE 2 AC1 5 HOH A 119 SITE 1 AC2 5 C A 5 G A 7 C A 8 HOH A 126 SITE 2 AC2 5 C B 5 CRYST1 53.730 19.390 45.830 90.00 105.70 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 0.018605 0.000000 0.005230 0.00000 SCALE2 0.000000 0.051546 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022660 0.00000