PDB Short entry for 2AZ0 HEADER VIRAL PROTEIN/RNA 09-SEP-05 2AZ0 TITLE FLOCK HOUSE VIRUS B2-DSRNA COMPLEX (P212121) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*CP*AP*(5BU)P*GP*GP*AP*CP*GP*CP*GP*(5BU) COMPND 3 P*CP*CP*AP*(5BU)P*GP*C)-3'; COMPND 4 CHAIN: C, D; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: B2 PROTEIN; COMPND 8 CHAIN: A, B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: FLOCK HOUSE VIRUS; SOURCE 5 ORGANISM_TAXID: 12287; SOURCE 6 GENE: B2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-RNA COMPLEX, FOUR-HELIX BUNDLE, VIRAL PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.A.CHAO,J.H.LEE,B.R.CHAPADOS,E.W.DEBLER,A.SCHNEEMANN,J.R.WILLIAMSON REVDAT 5 14-FEB-24 2AZ0 1 LINK REVDAT 4 24-FEB-09 2AZ0 1 VERSN REVDAT 3 31-JAN-06 2AZ0 1 JRNL REVDAT 2 18-OCT-05 2AZ0 1 REMARK REVDAT 1 11-OCT-05 2AZ0 0 JRNL AUTH J.A.CHAO,J.H.LEE,B.R.CHAPADOS,E.W.DEBLER,A.SCHNEEMANN, JRNL AUTH 2 J.R.WILLIAMSON JRNL TITL DUAL MODES OF RNA-SILENCING SUPPRESSION BY FLOCK HOUSE VIRUS JRNL TITL 2 PROTEIN B2. JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 952 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 16228003 JRNL DOI 10.1038/NSMB1005 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13054 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 632 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 : 1081 REMARK 3 NUCLEIC ACID ATOMS : 768 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 23 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) : 0.008 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 : 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 2AZ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034471. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9190 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 13519 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 34.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, MAGNESIUM SULFATE, PH 7, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.13050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.16900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.11600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.16900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.13050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.11600 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 LYS A 72 REMARK 465 ALA A 73 REMARK 465 MET B 1 REMARK 465 ALA B 73 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AZ2 RELATED DB: PDB REMARK 900 FLOCK HOUSE VIRUS B2-DSRNA COMPLEX (P4122) DBREF 2AZ0 A 1 73 UNP P68831 B2_FHV 1 73 DBREF 2AZ0 B 1 73 UNP P68831 B2_FHV 1 73 DBREF 2AZ0 C 1 18 PDB 2AZ0 2AZ0 1 18 DBREF 2AZ0 D 1 18 PDB 2AZ0 2AZ0 1 18 SEQRES 1 C 18 G C A 5BU G G A C G C G 5BU C SEQRES 2 C 18 C A 5BU G C SEQRES 1 D 18 G C A 5BU G G A C G C G 5BU C SEQRES 2 D 18 C A 5BU G C SEQRES 1 A 73 MET PRO SER LYS LEU ALA LEU ILE GLN GLU LEU PRO ASP SEQRES 2 A 73 ARG ILE GLN THR ALA VAL GLU ALA ALA MET GLY MET SER SEQRES 3 A 73 TYR GLN ASP ALA PRO ASN ASN VAL ARG ARG ASP LEU ASP SEQRES 4 A 73 ASN LEU HIS ALA CYS LEU ASN LYS ALA LYS LEU THR VAL SEQRES 5 A 73 SER ARG MET VAL THR SER LEU LEU GLU LYS PRO SER VAL SEQRES 6 A 73 VAL ALA TYR LEU GLU GLY LYS ALA SEQRES 1 B 73 MET PRO SER LYS LEU ALA LEU ILE GLN GLU LEU PRO ASP SEQRES 2 B 73 ARG ILE GLN THR ALA VAL GLU ALA ALA MET GLY MET SER SEQRES 3 B 73 TYR GLN ASP ALA PRO ASN ASN VAL ARG ARG ASP LEU ASP SEQRES 4 B 73 ASN LEU HIS ALA CYS LEU ASN LYS ALA LYS LEU THR VAL SEQRES 5 B 73 SER ARG MET VAL THR SER LEU LEU GLU LYS PRO SER VAL SEQRES 6 B 73 VAL ALA TYR LEU GLU GLY LYS ALA MODRES 2AZ0 5BU C 4 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE MODRES 2AZ0 5BU C 12 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE MODRES 2AZ0 5BU C 16 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE MODRES 2AZ0 5BU D 4 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE MODRES 2AZ0 5BU D 12 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE MODRES 2AZ0 5BU D 16 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE HET 5BU C 4 21 HET 5BU C 12 21 HET 5BU C 16 21 HET 5BU D 4 21 HET 5BU D 12 21 HET 5BU D 16 21 HETNAM 5BU 5-BROMO-URIDINE-5'-MONOPHOSPHATE FORMUL 1 5BU 6(C9 H12 BR N2 O9 P) FORMUL 5 HOH *23(H2 O) HELIX 1 1 SER A 3 GLU A 10 1 8 HELIX 2 2 GLU A 10 ALA A 21 1 12 HELIX 3 3 ALA A 22 MET A 25 5 4 HELIX 4 4 PRO A 31 LEU A 60 1 30 HELIX 5 5 LYS A 62 GLY A 71 1 10 HELIX 6 6 SER B 3 GLU B 10 1 8 HELIX 7 7 GLU B 10 MET B 25 1 16 HELIX 8 8 PRO B 31 GLU B 61 1 31 HELIX 9 9 LYS B 62 GLY B 71 1 10 LINK O3' A C 3 P 5BU C 4 1555 1555 1.61 LINK O3' 5BU C 4 P G C 5 1555 1555 1.61 LINK O3' G C 11 P 5BU C 12 1555 1555 1.61 LINK O3' 5BU C 12 P C C 13 1555 1555 1.60 LINK O3' A C 15 P 5BU C 16 1555 1555 1.60 LINK O3' 5BU C 16 P G C 17 1555 1555 1.60 LINK O3' A D 3 P 5BU D 4 1555 1555 1.61 LINK O3' 5BU D 4 P G D 5 1555 1555 1.60 LINK O3' G D 11 P 5BU D 12 1555 1555 1.61 LINK O3' 5BU D 12 P C D 13 1555 1555 1.60 LINK O3' A D 15 P 5BU D 16 1555 1555 1.60 LINK O3' 5BU D 16 P G D 17 1555 1555 1.60 CRYST1 50.261 86.232 94.338 90.00 90.00 90.00 P 21 21 21 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 0.019896 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011597 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010600 0.00000