HEADER ISOMERASE/RNA 22-MAY-09 3HJY TITLE STRUCTURE OF A FUNCTIONAL RIBONUCLEOPROTEIN PSEUDOURIDINE SYNTHASE TITLE 2 BOUND TO A SUBSTRATE RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSEUDOURIDINE SYNTHASE CBF5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CBF5; COMPND 5 SYNONYM: TRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE, TRNA-URIDINE COMPND 6 ISOMERASE, TRNA PSEUDOURIDYLATE SYNTHASE; COMPND 7 EC: 5.4.99.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RIBOSOME BIOGENESIS PROTEIN NOP10; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: NOP10; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-R(*GP*GP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*CP*CP*GP*CP*GP*GP COMPND 16 *CP*GP*C)-3'; COMPND 17 CHAIN: C; COMPND 18 FRAGMENT: GUIDE RNA_A; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: RNA (25-MER); COMPND 22 CHAIN: D; COMPND 23 FRAGMENT: GUIDE RNA_B; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 5; COMPND 26 MOLECULE: 5'-R(*GP*GP*AP*GP*CP*GP*UP*GP*CP*GP*GP*UP*UP*U)-3'; COMPND 27 CHAIN: E; COMPND 28 FRAGMENT: SUBSTRATE RNA; COMPND 29 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 STRAIN: DSM 3638; SOURCE 5 GENE: PF1785; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 12 ORGANISM_TAXID: 2261; SOURCE 13 STRAIN: DSM 3638; SOURCE 14 GENE: PF1141; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21 CODON PLUS; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 MOL_ID: 4; SOURCE 22 SYNTHETIC: YES; SOURCE 23 MOL_ID: 5; SOURCE 24 SYNTHETIC: YES KEYWDS PROTEIN-RNA COMPLEX, BOX H/ACA, RIBONUCLEOPROTEIN PARTICLES, RNP, KEYWDS 2 PSEUDOURIDINE SYNTHASE, PSEUDOURIDYLASE, PSEUDOURIDYLATION, RNA KEYWDS 3 EDITING, POST-TRANSCRIPTIONAL MODIFICATION, ISOMERASE, TRNA KEYWDS 4 PROCESSING, RIBONUCLEOPROTEIN, RIBOSOME BIOGENESIS, RRNA PROCESSING, KEYWDS 5 ISOMERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.LIANG,J.ZHOU,E.KAHEN,R.M.TERNS,M.P.TERNS,H.LI REVDAT 6 06-SEP-23 3HJY 1 REMARK REVDAT 5 24-JUL-19 3HJY 1 REMARK REVDAT 4 01-NOV-17 3HJY 1 REMARK REVDAT 3 13-JUL-11 3HJY 1 VERSN REVDAT 2 21-JUL-09 3HJY 1 JRNL REVDAT 1 23-JUN-09 3HJY 0 JRNL AUTH B.LIANG,J.ZHOU,E.KAHEN,R.M.TERNS,M.P.TERNS,H.LI JRNL TITL STRUCTURE OF A FUNCTIONAL RIBONUCLEOPROTEIN PSEUDOURIDINE JRNL TITL 2 SYNTHASE BOUND TO A SUBSTRATE RNA JRNL REF NAT.STRUCT.MOL.BIOL. V. 16 740 2009 JRNL REFN ISSN 1545-9993 JRNL PMID 19478803 JRNL DOI 10.1038/NSMB.1624 REMARK 2 REMARK 2 RESOLUTION. 3.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 3.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 22492 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) : 0.277 REMARK 3 R VALUE (WORKING SET) : 0.276 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1208 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) : 3.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1378 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.3290 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2989 REMARK 3 NUCLEIC ACID ATOMS : 1271 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 132.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.76000 REMARK 3 B22 (A**2) : -6.76000 REMARK 3 B33 (A**2) : 10.14000 REMARK 3 B12 (A**2) : -3.38000 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): 0.939 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.502 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.401 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 58.757 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.887 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.865 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4540 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6428 ; 1.505 ; 2.330 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 378 ; 6.922 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 132 ;37.603 ;22.727 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 576 ;21.598 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;22.314 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 759 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2945 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2013 ; 0.239 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2935 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 138 ; 0.158 ; 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): 34 ; 0.227 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.159 ; 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): 1961 ; 0.911 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3081 ; 1.656 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3352 ; 1.237 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3347 ; 2.270 ; 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 : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 11 A 337 REMARK 3 ORIGIN FOR THE GROUP (A):-112.9522 33.2712 39.7419 REMARK 3 T TENSOR REMARK 3 T11: 0.1911 T22: -0.1106 REMARK 3 T33: -0.0155 T12: -0.0702 REMARK 3 T13: 0.0264 T23: 0.1036 REMARK 3 L TENSOR REMARK 3 L11: 1.0264 L22: 3.8365 REMARK 3 L33: 1.5393 L12: -1.2537 REMARK 3 L13: 0.0114 L23: 1.7430 REMARK 3 S TENSOR REMARK 3 S11: 0.1338 S12: -0.3403 S13: -0.4038 REMARK 3 S21: 0.3159 S22: -0.2681 S23: 0.2813 REMARK 3 S31: 0.4491 S32: -0.3179 S33: 0.1344 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 55 REMARK 3 ORIGIN FOR THE GROUP (A):-104.6915 56.1007 37.0987 REMARK 3 T TENSOR REMARK 3 T11: -0.0503 T22: -0.0340 REMARK 3 T33: -0.2284 T12: 0.0361 REMARK 3 T13: 0.0452 T23: -0.0560 REMARK 3 L TENSOR REMARK 3 L11: 1.4062 L22: 2.7992 REMARK 3 L33: 10.2713 L12: 0.3171 REMARK 3 L13: -3.7500 L23: 0.0132 REMARK 3 S TENSOR REMARK 3 S11: -0.2371 S12: -0.2598 S13: -0.0856 REMARK 3 S21: -0.2306 S22: -0.1607 S23: -0.0745 REMARK 3 S31: -0.1285 S32: 0.1354 S33: 0.3978 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 21 REMARK 3 ORIGIN FOR THE GROUP (A):-126.0455 32.9520 18.4115 REMARK 3 T TENSOR REMARK 3 T11: 0.2518 T22: -0.4197 REMARK 3 T33: -0.0177 T12: 0.2554 REMARK 3 T13: -0.1199 T23: 0.1627 REMARK 3 L TENSOR REMARK 3 L11: 4.7505 L22: 12.7254 REMARK 3 L33: 2.9772 L12: -1.6039 REMARK 3 L13: 1.0614 L23: -2.0346 REMARK 3 S TENSOR REMARK 3 S11: 0.5259 S12: 1.2291 S13: 0.1199 REMARK 3 S21: -1.7875 S22: -0.5120 S23: 0.1109 REMARK 3 S31: 0.5789 S32: -0.5724 S33: -0.0139 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 25 REMARK 3 ORIGIN FOR THE GROUP (A):-118.5508 22.0237 24.4636 REMARK 3 T TENSOR REMARK 3 T11: 0.3491 T22: -0.5084 REMARK 3 T33: 0.2996 T12: 0.1187 REMARK 3 T13: -0.1369 T23: -0.0951 REMARK 3 L TENSOR REMARK 3 L11: 1.0503 L22: 5.2839 REMARK 3 L33: 1.6471 L12: 1.5111 REMARK 3 L13: -0.5624 L23: 1.2368 REMARK 3 S TENSOR REMARK 3 S11: 0.4969 S12: 0.5706 S13: -0.5601 REMARK 3 S21: -1.1096 S22: -0.8847 S23: 1.3033 REMARK 3 S31: 0.4562 S32: -0.4872 S33: 0.3878 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 4 E 16 REMARK 3 ORIGIN FOR THE GROUP (A):-132.4633 33.8007 18.0899 REMARK 3 T TENSOR REMARK 3 T11: 0.0184 T22: 0.0449 REMARK 3 T33: 0.5705 T12: 0.1582 REMARK 3 T13: -0.4329 T23: -0.2790 REMARK 3 L TENSOR REMARK 3 L11: 5.0715 L22: 23.9330 REMARK 3 L33: 5.7953 L12: -2.9436 REMARK 3 L13: 4.0126 L23: -9.9605 REMARK 3 S TENSOR REMARK 3 S11: 0.9091 S12: 1.1251 S13: -0.7200 REMARK 3 S21: -2.2567 S22: 0.1332 S23: 2.6641 REMARK 3 S31: 0.4488 S32: 0.4963 S33: -1.0423 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 3HJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000053225. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-08; 16-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 22-ID; 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL; NULL REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD; MARMOSAIC REMARK 200 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22492 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.650 REMARK 200 RESOLUTION RANGE LOW (A) : 49.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2EY4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0MM COCL2, 30MM CACL2, 2.0MM REMARK 280 SPERMINE, 2.0M LICL, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 84.91267 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 42.45633 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 84.91267 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.45633 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 84.91267 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 42.45633 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 84.91267 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 42.45633 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, 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 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 ARG A 146 REMARK 465 SER A 147 REMARK 465 ALA A 148 REMARK 465 VAL A 149 REMARK 465 LYS A 150 REMARK 465 ARG A 151 REMARK 465 ARG A 152 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 202 CG GLU A 202 CD 0.100 REMARK 500 G C 1 C2' G C 1 C1' 0.108 REMARK 500 G C 1 C2' G C 1 O2' 0.095 REMARK 500 G C 2 C2' G C 2 O2' 0.080 REMARK 500 C C 4 C2' C C 4 O2' 0.074 REMARK 500 REMARK 500 REMARK: NULL 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 PRO A 124 C - N - CA ANGL. DEV. = 11.3 DEGREES REMARK 500 PRO B 32 C - N - CA ANGL. DEV. = 18.5 DEGREES REMARK 500 PRO B 32 C - N - CD ANGL. DEV. = -14.5 DEGREES REMARK 500 U C 5 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 C D 7 O3' - P - OP2 ANGL. DEV. = 7.4 DEGREES REMARK 500 G D 8 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G D 8 C4 - C5 - N7 ANGL. DEV. = 2.5 DEGREES REMARK 500 G D 8 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 A D 21 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 G E 9 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 39 -76.21 -46.73 REMARK 500 LYS A 40 75.07 -105.13 REMARK 500 THR A 61 159.38 -48.41 REMARK 500 ASN A 74 59.38 30.47 REMARK 500 LYS A 77 104.12 56.21 REMARK 500 THR A 83 108.60 -55.80 REMARK 500 GLU A 97 -122.37 32.24 REMARK 500 PRO A 108 56.22 -96.35 REMARK 500 LEU A 116 74.15 -151.89 REMARK 500 HIS A 120 30.71 -87.57 REMARK 500 PRO A 124 115.12 -26.09 REMARK 500 GLU A 136 93.61 -44.96 REMARK 500 PRO A 143 -166.42 -78.31 REMARK 500 TYR A 160 146.24 -179.22 REMARK 500 ALA A 179 129.19 -38.04 REMARK 500 ARG A 204 134.24 -170.05 REMARK 500 GLU A 213 46.23 -90.90 REMARK 500 ASP A 214 -145.31 -90.99 REMARK 500 GLU A 237 -72.87 -22.63 REMARK 500 PRO A 275 34.56 -85.69 REMARK 500 THR A 316 11.50 -141.51 REMARK 500 MET A 328 128.92 -37.06 REMARK 500 ASP A 331 -14.35 -49.38 REMARK 500 LYS A 335 -71.96 -57.78 REMARK 500 LEU A 336 91.73 37.29 REMARK 500 THR B 15 154.28 177.79 REMARK 500 VAL B 22 -21.81 -34.33 REMARK 500 CYS B 23 -0.09 -157.05 REMARK 500 TYR B 41 0.01 59.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HJW RELATED DB: PDB REMARK 900 CBF5, NOP10, L7AE AND FULL-LENGTH PF9_PF6 COMPOSITE GUIDE RNA REMARK 900 COMPLEXED WITH THE SUBSTRATE RNA, CONTAINING 5-FLUORURIDINE AT THE REMARK 900 MODIFICATION POSITION DBREF 3HJY A 11 337 UNP Q7LWY0 TRUB_PYRFU 8 334 DBREF 3HJY B 3 55 UNP Q8U1R4 NOP10_PYRFU 3 55 DBREF 3HJY C 1 21 PDB 3HJY 3HJY 1 21 DBREF 3HJY D 1 25 PDB 3HJY 3HJY 1 25 DBREF 3HJY E 4 17 PDB 3HJY 3HJY 4 17 SEQRES 1 A 327 ARG ILE LEU PRO ALA ASP ILE LYS ARG GLU VAL LEU ILE SEQRES 2 A 327 LYS ASP GLU ASN ALA GLU THR ASN PRO ASP TRP GLY PHE SEQRES 3 A 327 PRO PRO GLU LYS ARG PRO ILE GLU MET HIS ILE GLN PHE SEQRES 4 A 327 GLY VAL ILE ASN LEU ASP LYS PRO PRO GLY PRO THR SER SEQRES 5 A 327 HIS GLU VAL VAL ALA TRP ILE LYS LYS ILE LEU ASN LEU SEQRES 6 A 327 GLU LYS ALA GLY HIS GLY GLY THR LEU ASP PRO LYS VAL SEQRES 7 A 327 SER GLY VAL LEU PRO VAL ALA LEU GLU LYS ALA THR ARG SEQRES 8 A 327 VAL VAL GLN ALA LEU LEU PRO ALA GLY LYS GLU TYR VAL SEQRES 9 A 327 ALA LEU MET HIS LEU HIS GLY ASP VAL PRO GLU ASP LYS SEQRES 10 A 327 ILE ILE GLN VAL MET LYS GLU PHE GLU GLY GLU ILE ILE SEQRES 11 A 327 GLN ARG PRO PRO LEU ARG SER ALA VAL LYS ARG ARG LEU SEQRES 12 A 327 ARG THR ARG LYS VAL TYR TYR ILE GLU VAL LEU GLU ILE SEQRES 13 A 327 GLU GLY ARG ASP VAL LEU PHE ARG VAL GLY VAL GLU ALA SEQRES 14 A 327 GLY THR TYR ILE ARG SER LEU ILE HIS HIS ILE GLY LEU SEQRES 15 A 327 ALA LEU GLY VAL GLY ALA HIS MET SER GLU LEU ARG ARG SEQRES 16 A 327 THR ARG SER GLY PRO PHE LYS GLU ASP GLU THR LEU ILE SEQRES 17 A 327 THR LEU HIS ASP LEU VAL ASP TYR TYR TYR PHE TRP LYS SEQRES 18 A 327 GLU ASP GLY ILE GLU GLU TYR PHE ARG LYS ALA ILE GLN SEQRES 19 A 327 PRO MET GLU LYS ALA VAL GLU HIS LEU PRO LYS VAL TRP SEQRES 20 A 327 ILE LYS ASP SER ALA VAL ALA ALA VAL THR HIS GLY ALA SEQRES 21 A 327 ASP LEU ALA VAL PRO GLY ILE ALA LYS LEU HIS ALA GLY SEQRES 22 A 327 ILE LYS ARG GLY ASP LEU VAL ALA ILE MET THR LEU LYS SEQRES 23 A 327 ASP GLU LEU VAL ALA LEU GLY LYS ALA MET MET THR SER SEQRES 24 A 327 GLN GLU MET LEU GLU LYS THR LYS GLY ILE ALA VAL ASP SEQRES 25 A 327 VAL GLU LYS VAL PHE MET PRO ARG ASP TRP TYR PRO LYS SEQRES 26 A 327 LEU TRP SEQRES 1 B 53 PHE ARG ILE ARG LYS CYS PRO LYS CYS GLY ARG TYR THR SEQRES 2 B 53 LEU LYS GLU VAL CYS PRO VAL CYS GLY GLU LYS THR LYS SEQRES 3 B 53 VAL ALA HIS PRO PRO ARG PHE SER PRO GLU ASP PRO TYR SEQRES 4 B 53 GLY GLU TYR ARG ARG ARG TRP LYS ARG GLU VAL LEU GLY SEQRES 5 B 53 ILE SEQRES 1 C 21 G G G C U C C G G A A A C SEQRES 2 C 21 C G C G G C G C SEQRES 1 D 25 G C G C U U C G C U C C C SEQRES 2 D 25 G G A G C C C A C A C U SEQRES 1 E 14 G G A G C G U G C G G U U SEQRES 2 E 14 U HELIX 1 1 PRO A 42 PHE A 49 1 8 HELIX 2 2 THR A 61 LEU A 73 1 13 HELIX 3 3 LYS A 98 ARG A 101 5 4 HELIX 4 4 VAL A 102 LEU A 107 1 6 HELIX 5 5 PRO A 124 LYS A 133 1 10 HELIX 6 6 TYR A 182 LEU A 194 1 13 HELIX 7 7 LEU A 220 GLU A 232 1 13 HELIX 8 8 GLU A 236 ALA A 242 1 7 HELIX 9 9 GLU A 247 VAL A 250 5 4 HELIX 10 10 LYS A 259 HIS A 268 1 10 HELIX 11 11 THR A 308 LYS A 315 1 8 HELIX 12 12 TYR B 41 GLY B 54 1 14 SHEET 1 A 7 VAL A 21 ILE A 23 0 SHEET 2 A 7 ILE A 277 HIS A 281 -1 O LEU A 280 N LEU A 22 SHEET 3 A 7 LYS A 255 ILE A 258 -1 N TRP A 257 O ALA A 278 SHEET 4 A 7 LEU A 289 MET A 293 1 O MET A 293 N ILE A 258 SHEET 5 A 7 LEU A 299 ALA A 305 -1 O VAL A 300 N ILE A 292 SHEET 6 A 7 ILE A 319 VAL A 326 -1 O LYS A 325 N LEU A 302 SHEET 7 A 7 LEU A 272 ALA A 273 -1 N LEU A 272 O ALA A 320 SHEET 1 B 4 ALA A 78 HIS A 80 0 SHEET 2 B 4 SER A 89 LEU A 96 -1 O ALA A 95 N GLY A 79 SHEET 3 B 4 GLY A 50 LYS A 56 -1 N ILE A 52 O VAL A 94 SHEET 4 B 4 ILE A 218 THR A 219 1 O ILE A 218 N ASN A 53 SHEET 1 C 8 GLY A 137 ILE A 140 0 SHEET 2 C 8 THR A 155 GLU A 167 -1 O ARG A 156 N ILE A 139 SHEET 3 C 8 ASP A 170 VAL A 177 -1 O ARG A 174 N GLU A 162 SHEET 4 C 8 LYS A 111 LEU A 119 -1 N ALA A 115 O PHE A 173 SHEET 5 C 8 ALA A 198 SER A 208 -1 O HIS A 199 N HIS A 118 SHEET 6 C 8 SER A 89 LEU A 96 1 N VAL A 91 O ARG A 205 SHEET 7 C 8 GLY A 50 LYS A 56 -1 N ILE A 52 O VAL A 94 SHEET 8 C 8 ILE A 243 PRO A 245 -1 O GLN A 244 N VAL A 51 SHEET 1 D 2 ARG B 6 LYS B 7 0 SHEET 2 D 2 LYS B 28 VAL B 29 -1 O LYS B 28 N LYS B 7 SSBOND 1 CYS B 8 CYS B 20 1555 1555 2.03 SSBOND 2 CYS B 11 CYS B 23 1555 1555 2.75 CRYST1 238.341 238.341 127.369 90.00 90.00 120.00 P 62 2 2 12 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 0.004196 0.002422 0.000000 0.00000 SCALE2 0.000000 0.004845 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007851 0.00000