HEADER RNA 24-AUG-07 2R22 TITLE STRUCTURE OF THE NATIVE RNA TRIDECAMER R(GCGUUUGAAACGC) AT TITLE 2 1.5 A (NATMN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*GP*CP*GP*UP*UP*UP*GP*AP*AP*AP*CP*GP*C)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS MONOVALENT, ELECTROSTATIC, ASYMMETRY, MANGANESE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR Y.TIMSIT,S.BOMBARD REVDAT 2 24-FEB-09 2R22 1 VERSN REVDAT 1 25-SEP-07 2R22 0 JRNL AUTH Y.TIMSIT,S.BOMBARD JRNL TITL THE 1.3 A STRUCTURE OF THE TRIDECAMER JRNL TITL 2 R(GCGUUUGAAACGC) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 104.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 63.3 REMARK 3 NUMBER OF REFLECTIONS : 12814 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) : 0.178 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1457 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 : 550 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.25700 REMARK 3 B22 (A**2) : 3.19300 REMARK 3 B33 (A**2) : 1.06400 REMARK 3 B12 (A**2) : -1.78900 REMARK 3 B13 (A**2) : -2.95400 REMARK 3 B23 (A**2) : 0.92900 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) : 0.004 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 40.16 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2R22 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-07. REMARK 100 THE RCSB ID CODE IS RCSB044327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.919487 REMARK 200 MONOCHROMATOR : SI (111) CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12814 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.7 REMARK 200 DATA REDUNDANCY : 1.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 6.40000 REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.10 REMARK 200 R MERGE FOR SHELL (I) : 0.27900 REMARK 200 R SYM FOR SHELL (I) : 19.70000 REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3 MM MNCL2, 100 MM NACL, 50 MM REMARK 280 TRIS, 30 % MPD, PH 7.0, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1850 ANGSTROM**2 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 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 NA A 14 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 4 O4 REMARK 620 2 U A 5 O4 73.0 REMARK 620 3 HOH A 51 O 109.1 87.1 REMARK 620 4 HOH A 37 O 141.1 75.2 91.1 REMARK 620 5 HOH A 48 O 96.2 155.0 75.1 121.6 REMARK 620 6 HOH B 69 O 75.8 100.1 172.4 88.3 98.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 15 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 7 N7 REMARK 620 2 HOH A 65 O 98.7 REMARK 620 3 HOH A 67 O 171.1 84.1 REMARK 620 4 HOH A 55 O 88.9 83.4 83.1 REMARK 620 5 HOH A 31 O 99.8 84.5 88.8 166.0 REMARK 620 6 HOH A 83 O 84.1 176.7 93.3 98.4 93.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 16 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 9 N7 REMARK 620 2 HOH A 64 O 93.0 REMARK 620 3 HOH A 75 O 167.5 76.7 REMARK 620 4 HOH A 50 O 93.4 82.4 92.2 REMARK 620 5 HOH A 73 O 82.2 86.8 90.1 168.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 1 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 17 O4 REMARK 620 2 U B 18 O4 81.9 REMARK 620 3 HOH B 61 O 100.3 165.3 REMARK 620 4 HOH B 42 O 153.8 76.3 104.4 REMARK 620 5 HOH B 62 O 101.9 85.5 79.8 90.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 17 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 30 O REMARK 620 2 HOH A 59 O 170.0 REMARK 620 3 HOH A 23 O 86.4 93.5 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2R1S RELATED DB: PDB REMARK 900 BROMINATED TRIDECAMER R(GCGUU-BRU-GAAACGC), 3MM MNCL2, 2 MM REMARK 900 MGCL2, RESOLUTION 1.4 A REMARK 900 RELATED ID: 2R20 RELATED DB: PDB REMARK 900 BROMINATED TRIDECAMER R(GCGUU-BRU-GAAACGC), 5MM MNCL2, 5MM REMARK 900 MGCL2, RESOLUTION 1.3 A REMARK 900 RELATED ID: 2R21 RELATED DB: PDB REMARK 900 BROMINATED TRIDECAMER R(GCGUU-BRU-GAAACGC), 0.5 MM MNCL2, REMARK 900 RESOLUTION 1.6 A DBREF 2R22 A 1 13 PDB 2R22 2R22 1 13 DBREF 2R22 B 14 26 PDB 2R22 2R22 14 26 SEQRES 1 A 13 G C G U U U G A A A C G C SEQRES 1 B 13 G C G U U U G A A A C G C HET NA B 1 1 HET NA A 14 1 HET NA A 15 1 HET NA A 16 1 HET MN A 17 1 HETNAM NA SODIUM ION HETNAM MN MANGANESE (II) ION FORMUL 3 NA 4(NA 1+) FORMUL 7 MN MN 2+ FORMUL 8 HOH *145(H2 O) LINK O4 U A 4 NA NA A 14 1555 1555 2.63 LINK O4 U A 5 NA NA A 14 1555 1555 2.73 LINK N7 G A 7 NA NA A 15 1555 1555 2.51 LINK N7 A A 9 NA NA A 16 1555 1555 2.75 LINK O4 U B 17 NA NA B 1 1555 1555 2.52 LINK O4 U B 18 NA NA B 1 1555 1555 2.38 LINK NA NA B 1 O HOH B 61 1555 1555 2.38 LINK NA NA B 1 O HOH B 42 1555 1555 2.51 LINK NA NA B 1 O HOH B 62 1555 1555 2.46 LINK NA NA A 14 O HOH A 51 1555 1555 2.38 LINK NA NA A 14 O HOH A 37 1555 1555 2.21 LINK NA NA A 14 O HOH A 48 1555 1555 2.39 LINK NA NA A 14 O HOH B 69 1555 1555 2.94 LINK NA NA A 15 O HOH A 65 1555 1555 2.46 LINK NA NA A 15 O HOH A 67 1555 1555 2.55 LINK NA NA A 15 O HOH A 55 1555 1555 2.57 LINK NA NA A 15 O HOH A 31 1555 1555 2.41 LINK NA NA A 15 O HOH A 83 1555 1555 2.38 LINK NA NA A 16 O HOH A 64 1555 1555 2.71 LINK NA NA A 16 O HOH A 75 1555 1555 2.47 LINK NA NA A 16 O HOH A 50 1555 1555 2.39 LINK NA NA A 16 O HOH A 73 1555 1555 2.27 LINK MN MN A 17 O HOH A 30 1555 1555 2.10 LINK MN MN A 17 O HOH A 59 1555 1555 1.95 LINK MN MN A 17 O HOH A 23 1555 1555 2.26 CRYST1 25.280 25.500 29.600 97.97 106.69 101.62 P 1 2 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 0.039557 0.008134 0.013871 0.00000 SCALE2 0.000000 0.040036 0.008575 0.00000 SCALE3 0.000000 0.000000 0.036070 0.00000 MASTER 271 0 5 0 0 0 0 6 0 0 0 2 END