PDB Short entry for 1QBP HEADER RNA 26-APR-99 1QBP TITLE CRYSTAL STRUCTURE OF A BROMINATED RNA HELIX WITH FOUR TITLE 2 MISMATCHED BASE PAIRS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*UP*GP*(CBV)P*(CBV) COMPND 3 P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'; COMPND 4 CHAIN: A, B, C, D, E, F; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED BY THE SOLID-PHASE SOURCE 4 PHOSPHORAMIDITE METHOD KEYWDS BROMINATED CYTOSINE, MISMATCHED BASE PAIRS, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.C.ANDERSON,R.H.O'NEIL,D.J.FILMAN,C.A.FREDERICK REVDAT 5 24-FEB-09 1QBP 1 VERSN REVDAT 4 01-APR-03 1QBP 1 JRNL REVDAT 3 28-JUN-02 1QBP 1 REMARK REVDAT 2 27-NOV-00 1QBP 5 REVDAT 1 26-NOV-99 1QBP 0 JRNL AUTH A.C.ANDERSON,R.H.O'NEIL,D.J.FILMAN,C.A.FREDERICK JRNL TITL CRYSTAL STRUCTURE OF A BROMINATED RNA HELIX WITH JRNL TITL 2 FOUR MISMATCHED BASE PAIRS: AN INVESTIGATION INTO JRNL TITL 3 RNA CONFORMATIONAL VARIABILITY. JRNL REF BIOCHEMISTRY V. 38 12577 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10504226 JRNL DOI 10.1021/BI9904508 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 999.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 11919 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1192 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1800 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 110 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QBP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-99. REMARK 100 THE RCSB ID CODE IS RCSB009050. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL1-5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92036 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11919 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 MM SODIUM CACODYLATE, 45 MM REMARK 280 MGCL2, 60 MM SPERMINE, 6.7 % MPD, RESERVOIR 40 % MPD, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K 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 52.22500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 12.13500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.22500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 12.13500 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, 3 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 U A 1 O5' C5' C4' O4' C3' C2' O2' REMARK 470 U A 1 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U A 1 C5 C6 REMARK 470 U B 16 O5' C5' C4' O4' C3' C2' O2' REMARK 470 U B 16 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U B 16 C5 C6 REMARK 470 U C 31 O5' C5' C4' O4' C3' C2' O2' REMARK 470 U C 31 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U C 31 C5 C6 REMARK 470 U D 46 O5' C5' C4' O4' C3' C2' O2' REMARK 470 U D 46 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U D 46 C5 C6 REMARK 470 U E 61 O5' C5' C4' O4' C3' C2' O2' REMARK 470 U E 61 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U E 61 C5 C6 REMARK 470 U F 76 O5' C5' C4' O4' C3' C2' O2' REMARK 470 U F 76 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U F 76 C5 C6 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 B6220 DISTANCE = 5.72 ANGSTROMS REMARK 525 HOH D6085 DISTANCE = 5.36 ANGSTROMS DBREF 1QBP A 1 15 PDB 1QBP 1QBP 1 15 DBREF 1QBP B 16 30 PDB 1QBP 1QBP 16 30 DBREF 1QBP C 31 45 PDB 1QBP 1QBP 31 45 DBREF 1QBP D 46 60 PDB 1QBP 1QBP 46 60 DBREF 1QBP E 61 75 PDB 1QBP 1QBP 61 75 DBREF 1QBP F 76 90 PDB 1QBP 1QBP 76 90 SEQRES 1 A 15 U G CBV CBV A G U U C G C U G SEQRES 2 A 15 G C SEQRES 1 B 15 U G CBV CBV A G U U C G C U G SEQRES 2 B 15 G C SEQRES 1 C 15 U G CBV CBV A G U U C G C U G SEQRES 2 C 15 G C SEQRES 1 D 15 U G CBV CBV A G U U C G C U G SEQRES 2 D 15 G C SEQRES 1 E 15 U G CBV CBV A G U U C G C U G SEQRES 2 E 15 G C SEQRES 1 F 15 U G CBV CBV A G U U C G C U G SEQRES 2 F 15 G C MODRES 1QBP CBV A 3 C MODRES 1QBP CBV A 4 C MODRES 1QBP CBV B 18 C MODRES 1QBP CBV B 19 C MODRES 1QBP CBV C 33 C MODRES 1QBP CBV C 34 C MODRES 1QBP CBV D 48 C MODRES 1QBP CBV D 49 C MODRES 1QBP CBV E 63 C MODRES 1QBP CBV E 64 C MODRES 1QBP CBV F 78 C MODRES 1QBP CBV F 79 C HET CBV A 3 21 HET CBV A 4 21 HET CBV B 18 21 HET CBV B 19 21 HET CBV C 33 21 HET CBV C 34 21 HET CBV D 48 21 HET CBV D 49 21 HET CBV E 63 21 HET CBV E 64 21 HET CBV F 78 21 HET CBV F 79 21 HETNAM CBV 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) FORMUL 1 CBV 12(C9 H13 BR N3 O8 P) FORMUL 7 HOH *110(H2 O) LINK O3' G A 2 P CBV A 3 1555 1555 1.60 LINK O3' CBV A 3 P CBV A 4 1555 1555 1.61 LINK O3' CBV A 4 P A A 5 1555 1555 1.59 LINK O3' G B 17 P CBV B 18 1555 1555 1.59 LINK O3' CBV B 18 P CBV B 19 1555 1555 1.58 LINK O3' CBV B 19 P A B 20 1555 1555 1.60 LINK O3' G C 32 P CBV C 33 1555 1555 1.61 LINK O3' CBV C 33 P CBV C 34 1555 1555 1.59 LINK O3' CBV C 34 P A C 35 1555 1555 1.60 LINK O3' G D 47 P CBV D 48 1555 1555 1.60 LINK O3' CBV D 48 P CBV D 49 1555 1555 1.59 LINK O3' CBV D 49 P A D 50 1555 1555 1.60 LINK O3' G E 62 P CBV E 63 1555 1555 1.60 LINK O3' CBV E 63 P CBV E 64 1555 1555 1.62 LINK O3' CBV E 64 P A E 65 1555 1555 1.59 LINK O3' G F 77 P CBV F 78 1555 1555 1.61 LINK O3' CBV F 78 P CBV F 79 1555 1555 1.63 LINK O3' CBV F 79 P A F 80 1555 1555 1.61 CRYST1 104.450 24.270 104.450 90.00 118.76 90.00 C 1 2 1 24 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 0.009574 0.000000 0.005255 0.00000 SCALE2 0.000000 0.041203 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010921 0.00000