HEADER RNA 14-MAY-99 1QCU TITLE CRYSTAL STRUCTURE OF AN 18 BASE PAIR COPY CONTROL RELATED RNA DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3'; COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'; COMPND 7 CHAIN: B, C; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS A-RNA STRUCTURE, RIBONUCLEIC ACID, RNA EXPDTA X-RAY DIFFRACTION AUTHOR P.S.KLOSTERMAN,S.A.SHAH,T.A.STEITZ REVDAT 5 03-APR-24 1QCU 1 REMARK REVDAT 4 14-FEB-24 1QCU 1 REMARK REVDAT 3 24-FEB-09 1QCU 1 VERSN REVDAT 2 31-JUL-00 1QCU 3 ATOM REMARK REVDAT 1 11-NOV-99 1QCU 0 JRNL AUTH P.S.KLOSTERMAN,S.A.SHAH,T.A.STEITZ JRNL TITL CRYSTAL STRUCTURES OF TWO PLASMID COPY CONTROL RELATED RNA JRNL TITL 2 DUPLEXES: AN 18 BASE PAIR DUPLEX AT 1.20 A RESOLUTION AND A JRNL TITL 3 19 BASE PAIR DUPLEX AT 1.55 A RESOLUTION. JRNL REF BIOCHEMISTRY V. 38 14784 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10555960 JRNL DOI 10.1021/BI9912793 REMARK 2 REMARK 2 RESOLUTION. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.118 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.116 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 909 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 18266 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.109 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.108 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.141 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 791 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 15712 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 946 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 195 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 578.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 227.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 22 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7977 REMARK 3 NUMBER OF RESTRAINTS : 21649 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.027 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.029 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.026 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.086 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL., 91 201-228 (1973) REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : PARKINSON ET AL. REMARK 3 SPECIAL CASE: USED THE AVERAGE OF GUA C6 O6, ADE C6 N6 BOND REMARK 3 LENGTHS AS THE C6 O6 BOND LENGTH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 6.5% REMARK 3 REMARK 3 THE MOLECULE CRYSTALLIZED IN SPACE GROUP P321. HOWEVER REMARK 3 THE REFINEMENT WAS CARRIED OUT IN THE LOWER SPACE GROUP REMARK 3 P3. THE COORDINATES DEPOSITED ARE FOR THE SPACE GROUP P3. REMARK 4 REMARK 4 1QCU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000009091. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-97; 06-JUL-97 REMARK 200 TEMPERATURE (KELVIN) : 100.0; 100.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : CHESS; ROTATING ANODE REMARK 200 BEAMLINE : A1; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9140; 1.5418 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K; RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18266 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.27400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: A-RNA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (NH4)2SO4, SODIUM CACODYLATE, MGCL2, REMARK 280 ROP PROTEIN, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 N NH4 A 202 LIES ON A SPECIAL POSITION. REMARK 375 N NH4 A 203 LIES ON A SPECIAL POSITION. REMARK 375 N NH4 B 201 LIES ON A SPECIAL POSITION. REMARK 375 N NH4 B 204 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 206 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 207 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 205 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 208 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 332 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 352 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 THE CRYSTALS EXHIBIT 36-FOLD STATIC DISORDER, SUCH THAT REMARK 400 THERE IS ONE CONFORMATION OF THE SUGAR-PHOSPHATE BACKBONE REMARK 400 BUT THE BASE COMPOSITION IS AVERAGED AT EACH POSITION. REMARK 400 REMARK 400 THE CRYSTALS WERE GROWN FROM TWO 18MER OLIGORIBONUCLEOTIDES, REMARK 400 WITH SEQUENCES 5'-R(*CP*AP*CP*CP*GP*UP*UP*GP*GP*UP*AP*GP* REMARK 400 CP*GP*GP*UP*GP*C)-3' AND 5'-R(*CP*AP*CP*CP*GP*CP*UP*AP*CP* REMARK 400 CP*AP*AP*CP*GP*GP*UP*GP*C)-3' RESPECTIVELY. THESE REMARK 400 SEQUENCES OCCUR NATURALLY IN E. COLI. REMARK 400 REMARK 400 THE AVERAGING PRODUCES CRYSTALS WITH ONE TURN, 11 BASE REMARK 400 PAIRS, OF A RNA IN THE ASYMMETRIC UNIT. THIS IS MODELED REMARK 400 USING ONE G AND ONE C RESIDUE CONNECTED TO EACH RIBOSE C1*, REMARK 400 WITH PARTIAL OCCUPANCIES EQUAL TO THE FREQUENCIES OF REMARK 400 PURINES AND PYRIMIDINES, RESPECTIVELY, IN THE 18MER DUPLEX. REMARK 400 STRAND A, ALL G'S, AND STRAND C, ALL C'S, HAVE IDENTICAL REMARK 400 RIBOSE AND PHOSPHATE COORDINATES AND ATOMIC DISPLACEMENT REMARK 400 PARAMETERS; LIKEWISE STRAND B, ALL C'S, AND STRAND D, ALL REMARK 400 G'S, HAVE IDENTICAL SUGAR - PHOSPHATE BACKBONES. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH4 B 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QC0 RELATED DB: PDB REMARK 900 1QC0 CONTAINS THE SAME RNA SEQUENCES WITH BOTH STRANDS CONTAINING REMARK 900 AN ADDITIONAL 5' TERMINAL G DBREF 1QCU A 1 11 PDB 1QCU 1QCU 1 11 DBREF 1QCU B 12 22 PDB 1QCU 1QCU 12 22 DBREF 1QCU C 101 111 PDB 1QCU 1QCU 101 111 DBREF 1QCU D 112 122 PDB 1QCU 1QCU 112 122 SEQRES 1 A 11 G G G G G G G G G G G SEQRES 1 B 11 C C C C C C C C C C C SEQRES 1 C 11 C C C C C C C C C C C SEQRES 1 D 11 G G G G G G G G G G G HET NH4 A 202 1 HET NH4 A 203 1 HET NH4 B 201 1 HET NH4 B 204 1 HETNAM NH4 AMMONIUM ION FORMUL 5 NH4 4(H4 N 1+) FORMUL 9 HOH *195(H2 O) SITE 1 AC1 2 C B 22 G D 122 SITE 1 AC2 2 G A 5 C C 105 SITE 1 AC3 2 G A 11 C C 111 SITE 1 AC4 2 C B 16 G D 116 CRYST1 43.806 43.806 29.170 90.00 90.00 120.00 P 3 6 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 0.022828 0.013180 0.000000 0.00000 SCALE2 0.000000 0.026359 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034282 0.00000