HEADER RNA 15-MAR-12 4E6B TITLE CRYSTAL STRUCTURE OF STATISTICALLY DISORDERED 19MER DUPLEX P(CGG) TITLE 2 3C(CUG)3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(P*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*U COMPND 3 P*G)-3'; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: SEE REMARK 999; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: P(CGG)3C(CUG)3; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-R(P*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*U COMPND 10 P*G)-3'; COMPND 11 CHAIN: F, E; COMPND 12 FRAGMENT: SEE REMARK 999; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: P(CGG)3C(CUG)3 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS SIRNA, TRINUCLEOTIDE REPEAT EXPANSION, RNA EXPDTA X-RAY DIFFRACTION AUTHOR L.MALININA,A.POPOV,J.TAMJAR REVDAT 4 28-FEB-24 4E6B 1 REMARK REVDAT 3 15-NOV-17 4E6B 1 REMARK REVDAT 2 29-AUG-12 4E6B 1 JRNL REVDAT 1 11-JUL-12 4E6B 0 JRNL AUTH J.TAMJAR,E.KATORCHA,A.POPOV,L.MALININA JRNL TITL STRUCTURAL DYNAMICS OF DOUBLE-HELICAL RNAS COMPOSED OF JRNL TITL 2 CUG/CUG- AND CUG/CGG-REPEATS. JRNL REF J.BIOMOL.STRUCT.DYN. V. 30 505 2012 JRNL REFN ISSN 0739-1102 JRNL PMID 22731704 JRNL DOI 10.1080/07391102.2012.687517 REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 3481 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 152 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 247 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 13 REMARK 3 BIN FREE R VALUE : 0.1940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 344 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.01000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 382 ; 0.020 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 128 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 592 ; 1.859 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 336 ; 1.673 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 80 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 168 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 32 ; 0.012 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 14 ; 0.060 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 106 ; 0.192 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 137 ; 0.239 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 82 ; 0.059 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 3 ; 0.031 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 2 ; 0.115 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 2 ; 0.528 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.005 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 382 ; 1.329 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 592 ; 1.903 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4E6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071223. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9724 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3488 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.16900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9 MM AMMONIUM SULFATE, 5% REMARK 280 ISOPROPANOL, PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 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 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 SMTRY1 4 1.000000 0.000000 0.000000 19.88950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 11.48321 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.63333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 19.88950 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 11.48321 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 11.63333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 19.88950 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 11.48321 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 11.63333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 22.96642 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 23.26667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 22.96642 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 23.26667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 22.96642 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 23.26667 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 BIOLOGICAL ASSEMBLY IS A 19-MER RNA DUPLEX. DUE TO REMARK 300 STATISTICAL DISORDER WITHIN THE CRYSTAL, REMARK 350 REPRESENTS THE REMARK 300 ASYMMETRIC UNIT. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, F, E 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 HOH A 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 102 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 106 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 102 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 103 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 104 LIES ON A SPECIAL POSITION. 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 B 10 N1 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4E48 RELATED DB: PDB REMARK 900 RELATED ID: 4E5C RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 IN THE CRYSTAL, RNA 19-MER P(CGG)3C(CUG)3 PACKS IN A PSEUDO- REMARK 999 CONTINUOUS DOUBLE HELIX WITH A 4-BASE ASYMMETRIC UNIT. TO BEST REMARK 999 REPRESENT THE ARRANGEMENT OF THE BASES, THE RNA HAS BEEN MODELED AS REMARK 999 TWO OVERLAPPING (WITH THE APPLICATION OF CRYSTAL SYMMETRY) SELF- REMARK 999 COMPLEMENTARY TETRAMER DUPLEXES WITH OCCUPANCY 0.5. DBREF 4E6B A 8 11 PDB 4E6B 4E6B 8 11 DBREF 4E6B B 7 10 PDB 4E6B 4E6B 7 10 DBREF 4E6B F 8 11 PDB 4E6B 4E6B 8 11 DBREF 4E6B E 7 10 PDB 4E6B 4E6B 7 10 SEQRES 1 A 4 C G C G SEQRES 1 B 4 C G C G SEQRES 1 F 4 G C G C SEQRES 1 E 4 G C G C FORMUL 5 HOH *18(H2 O) CRYST1 39.779 39.779 34.900 90.00 90.00 120.00 H 3 18 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 0.025139 0.014514 0.000000 0.00000 SCALE2 0.000000 0.029028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028653 0.00000