HEADER ISOMERASE/RNA 30-SEP-07 2RFK TITLE SUBSTRATE RNA POSITIONING IN THE ARCHAEAL H/ACA RIBONUCLEOPROTEIN TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUIDE RNA 1; COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GUIDE RNA 2; COMPND 7 CHAIN: E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: TARGET RNA; COMPND 11 CHAIN: F; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: PROBABLE TRNA PSEUDOURIDINE SYNTHASE B; COMPND 15 CHAIN: A; COMPND 16 SYNONYM: TRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE, TRNA-URIDINE COMPND 17 ISOMERASE, TRNA PSEUDOURIDYLATE SYNTHASE; COMPND 18 EC: 5.4.99.-; COMPND 19 ENGINEERED: YES; COMPND 20 MUTATION: YES; COMPND 21 MOL_ID: 5; COMPND 22 MOLECULE: RIBOSOME BIOGENESIS PROTEIN NOP10; COMPND 23 CHAIN: B; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 6; COMPND 26 MOLECULE: SMALL NUCLEOLAR RNP SIMILAR TO GAR1; COMPND 27 CHAIN: C; COMPND 28 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 9 ORGANISM_TAXID: 2261; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET; SOURCE 14 MOL_ID: 5; SOURCE 15 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 16 ORGANISM_TAXID: 2261; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET; SOURCE 21 MOL_ID: 6; SOURCE 22 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 23 ORGANISM_TAXID: 2261; SOURCE 24 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 25 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 26 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 27 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS PROTEIN-RNA COMPLEX, ARCHAEAL H-ACA RIBONUCLEOPROTEIN COMPLEX, KEYWDS 2 ISOMERASE, TRNA PROCESSING, RIBOSOME BIOGENESIS, RRNA PROCESSING, KEYWDS 3 ISOMERASE-RNA COMPLEX, STRUCTURAL GENOMICS, SOUTHEAST COLLABORATORY KEYWDS 4 FOR STRUCTURAL GENOMICS, SECSG, PSI-2, PROTEIN STRUCTURE INITIATIVE EXPDTA X-RAY DIFFRACTION AUTHOR B.LIANG,S.XUE,R.M.TERNS,M.P.TERNS,H.LI,SOUTHEAST COLLABORATORY FOR AUTHOR 2 STRUCTURAL GENOMICS (SECSG) REVDAT 5 30-AUG-23 2RFK 1 REMARK REVDAT 4 20-OCT-21 2RFK 1 REMARK SEQADV LINK REVDAT 3 20-OCT-09 2RFK 1 JRNL REVDAT 2 24-FEB-09 2RFK 1 VERSN REVDAT 1 05-FEB-08 2RFK 0 JRNL AUTH B.LIANG,S.XUE,R.M.TERNS,M.P.TERNS,H.LI JRNL TITL SUBSTRATE RNA POSITIONING IN THE ARCHAEAL H/ACA JRNL TITL 2 RIBONUCLEOPROTEIN COMPLEX. JRNL REF NAT.STRUCT.MOL.BIOL. V. 14 1189 2007 JRNL REFN ISSN 1545-9993 JRNL PMID 18059286 JRNL DOI 10.1038/NSMB1336 REMARK 2 REMARK 2 RESOLUTION. 2.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 3 NUMBER OF REFLECTIONS : 20534 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) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1019 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) : 2.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 667 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 35.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.4050 REMARK 3 BIN FREE R VALUE SET COUNT : 36 REMARK 3 BIN FREE R VALUE : 0.4210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3711 REMARK 3 NUCLEIC ACID ATOMS : 1293 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.54000 REMARK 3 B22 (A**2) : 6.54000 REMARK 3 B33 (A**2) : -13.09000 REMARK 3 B12 (A**2) : 0.00000 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): 2.430 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.466 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.460 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 56.708 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5247 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7389 ; 1.725 ; 2.291 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 458 ; 7.092 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;37.831 ;22.733 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 704 ;21.588 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;15.798 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 866 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3455 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2525 ; 0.239 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3425 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 171 ; 0.181 ; 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): 46 ; 0.192 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.238 ; 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): 2357 ; 0.385 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3745 ; 0.706 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3690 ; 0.876 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3642 ; 1.547 ; 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 : 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 2RFK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000044797. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20534 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.870 REMARK 200 RESOLUTION RANGE LOW (A) : 42.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 15.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11000 REMARK 200 FOR THE DATA SET : 41.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 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 (%): 68.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM MES, 100 MM NH4COOCH3, 5 MM REMARK 280 MGSO4, 1.0 M NACL, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 120.48900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 48.28050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.28050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.24450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.28050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.28050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 180.73350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.28050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.28050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.24450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.28050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.28050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 180.73350 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 120.48900 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11200 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F, A, B, C 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS B 8 SG CYS B 20 2.03 REMARK 500 O ARG A 41 NH2 ARG A 240 2.09 REMARK 500 SG CYS B 8 SG CYS B 11 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 C 74 CD GLU C 74 OE1 0.238 REMARK 500 GLU C 74 CD GLU C 74 OE2 0.231 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 U D 5 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 C E 12 C3' - C2' - C1' ANGL. DEV. = -4.7 DEGREES REMARK 500 G F 4 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 CYS B 8 CA - CB - SG ANGL. DEV. = 8.6 DEGREES REMARK 500 CYS B 23 CA - CB - SG ANGL. DEV. = 11.1 DEGREES REMARK 500 GLU C 74 OE1 - CD - OE2 ANGL. DEV. = 10.0 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 ILE A 17 119.07 -38.28 REMARK 500 PRO A 38 -91.08 -31.68 REMARK 500 GLU A 39 27.23 -61.54 REMARK 500 LYS A 40 52.85 -150.45 REMARK 500 GLU A 97 -114.66 48.20 REMARK 500 VAL A 103 -52.01 -16.10 REMARK 500 GLN A 104 -67.88 -27.48 REMARK 500 ALA A 105 -37.09 -30.99 REMARK 500 HIS A 120 53.75 -104.96 REMARK 500 ILE A 129 5.12 -64.16 REMARK 500 PRO A 144 -122.88 -94.80 REMARK 500 LEU A 145 94.97 -4.11 REMARK 500 ARG A 146 -125.38 -111.80 REMARK 500 ALA A 148 89.30 -64.33 REMARK 500 ARG A 151 -156.24 -92.05 REMARK 500 ARG A 152 -176.47 36.05 REMARK 500 ALA A 179 -85.81 -10.13 REMARK 500 GLU A 215 -5.25 -52.55 REMARK 500 ALA A 249 3.82 -64.26 REMARK 500 VAL A 300 -53.10 -120.87 REMARK 500 GLN A 310 -27.32 -39.33 REMARK 500 PHE A 327 -61.52 -90.75 REMARK 500 LYS A 339 -155.03 -78.64 REMARK 500 GLU B 25 -163.65 -76.07 REMARK 500 ASP B 39 62.53 37.25 REMARK 500 HIS C 9 -173.92 -176.59 REMARK 500 PRO C 24 -128.12 -83.39 REMARK 500 LYS C 33 -2.55 -50.39 REMARK 500 VAL C 38 -61.16 -100.60 REMARK 500 PRO C 47 118.20 -37.92 REMARK 500 PRO C 51 -166.80 -77.42 REMARK 500 REMARK 500 REMARK: NULL 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 ZN B 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 8 SG REMARK 620 2 CYS B 11 SG 53.8 REMARK 620 3 CYS B 23 SG 51.2 53.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: PFU-1661227-001 RELATED DB: TARGETDB REMARK 900 RELATED ID: PFU-1095826-001 RELATED DB: TARGETDB REMARK 900 RELATED ID: PFU-1665068-001 RELATED DB: TARGETDB DBREF 2RFK A 8 341 UNP Q7LWY0 TRUB_PYRFU 5 338 DBREF 2RFK B 3 55 UNP Q8U1R4 NOP10_PYRFU 3 55 DBREF 2RFK C 1 74 UNP Q8U029 Q8U029_PYRFU 8 81 DBREF 2RFK D 1 21 PDB 2RFK 2RFK 1 21 DBREF 2RFK E 1 26 PDB 2RFK 2RFK 1 26 DBREF 2RFK F 4 17 PDB 2RFK 2RFK 4 17 SEQADV 2RFK ALA A 85 UNP Q7LWY0 ASP 82 ENGINEERED MUTATION SEQRES 1 D 21 G G G C U C C G G A A A C SEQRES 2 D 21 C G C G G C G C SEQRES 1 E 26 G C G C U U C G C U C C C SEQRES 2 E 26 G G A G C C C A C A C U A SEQRES 1 F 14 G G A G C G U G C G G U U SEQRES 2 F 14 U SEQRES 1 A 334 GLU VAL ARG ARG ILE LEU PRO ALA ASP ILE LYS ARG GLU SEQRES 2 A 334 VAL LEU ILE LYS ASP GLU ASN ALA GLU THR ASN PRO ASP SEQRES 3 A 334 TRP GLY PHE PRO PRO GLU LYS ARG PRO ILE GLU MET HIS SEQRES 4 A 334 ILE GLN PHE GLY VAL ILE ASN LEU ASP LYS PRO PRO GLY SEQRES 5 A 334 PRO THR SER HIS GLU VAL VAL ALA TRP ILE LYS LYS ILE SEQRES 6 A 334 LEU ASN LEU GLU LYS ALA GLY HIS GLY GLY THR LEU ALA SEQRES 7 A 334 PRO LYS VAL SER GLY VAL LEU PRO VAL ALA LEU GLU LYS SEQRES 8 A 334 ALA THR ARG VAL VAL GLN ALA LEU LEU PRO ALA GLY LYS SEQRES 9 A 334 GLU TYR VAL ALA LEU MET HIS LEU HIS GLY ASP VAL PRO SEQRES 10 A 334 GLU ASP LYS ILE ILE GLN VAL MET LYS GLU PHE GLU GLY SEQRES 11 A 334 GLU ILE ILE GLN ARG PRO PRO LEU ARG SER ALA VAL LYS SEQRES 12 A 334 ARG ARG LEU ARG THR ARG LYS VAL TYR TYR ILE GLU VAL SEQRES 13 A 334 LEU GLU ILE GLU GLY ARG ASP VAL LEU PHE ARG VAL GLY SEQRES 14 A 334 VAL GLU ALA GLY THR TYR ILE ARG SER LEU ILE HIS HIS SEQRES 15 A 334 ILE GLY LEU ALA LEU GLY VAL GLY ALA HIS MET SER GLU SEQRES 16 A 334 LEU ARG ARG THR ARG SER GLY PRO PHE LYS GLU ASP GLU SEQRES 17 A 334 THR LEU ILE THR LEU HIS ASP LEU VAL ASP TYR TYR TYR SEQRES 18 A 334 PHE TRP LYS GLU ASP GLY ILE GLU GLU TYR PHE ARG LYS SEQRES 19 A 334 ALA ILE GLN PRO MET GLU LYS ALA VAL GLU HIS LEU PRO SEQRES 20 A 334 LYS VAL TRP ILE LYS ASP SER ALA VAL ALA ALA VAL THR SEQRES 21 A 334 HIS GLY ALA ASP LEU ALA VAL PRO GLY ILE ALA LYS LEU SEQRES 22 A 334 HIS ALA GLY ILE LYS ARG GLY ASP LEU VAL ALA ILE MET SEQRES 23 A 334 THR LEU LYS ASP GLU LEU VAL ALA LEU GLY LYS ALA MET SEQRES 24 A 334 MET THR SER GLN GLU MET LEU GLU LYS THR LYS GLY ILE SEQRES 25 A 334 ALA VAL ASP VAL GLU LYS VAL PHE MET PRO ARG ASP TRP SEQRES 26 A 334 TYR PRO LYS LEU TRP GLU LYS ARG ASP 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 74 MET LYS ARG LEU GLY LYS VAL LEU HIS TYR ALA LYS GLN SEQRES 2 C 74 GLY PHE LEU ILE VAL ARG THR ASN TRP VAL PRO SER LEU SEQRES 3 C 74 ASN ASP ARG VAL VAL ASP LYS ARG LEU GLN PHE VAL GLY SEQRES 4 C 74 ILE VAL LYS ASP VAL PHE GLY PRO VAL LYS MET PRO TYR SEQRES 5 C 74 VAL ALA ILE LYS PRO LYS VAL SER ASN PRO GLU ILE TYR SEQRES 6 C 74 VAL GLY GLU VAL LEU TYR VAL ASP GLU HET ZN B 1 1 HETNAM ZN ZINC ION FORMUL 7 ZN ZN 2+ HELIX 1 1 PRO A 42 PHE A 49 1 8 HELIX 2 2 THR A 61 ASN A 74 1 14 HELIX 3 3 LYS A 98 LEU A 107 5 10 HELIX 4 4 PRO A 124 PHE A 135 1 12 HELIX 5 5 ILE A 183 GLY A 195 1 13 HELIX 6 6 LEU A 220 GLU A 232 1 13 HELIX 7 7 ILE A 235 ALA A 242 1 8 HELIX 8 8 GLU A 247 GLU A 251 5 5 HELIX 9 9 LYS A 259 HIS A 268 1 10 HELIX 10 10 THR A 308 LEU A 313 1 6 HELIX 11 11 TYR B 41 LEU B 53 1 13 HELIX 12 12 PRO C 62 VAL C 66 5 5 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 LYS A 279 SHEET 4 A 7 LEU A 289 THR A 294 1 O MET A 293 N VAL A 256 SHEET 5 A 7 LEU A 299 ALA A 305 -1 O ALA A 301 N ILE A 292 SHEET 6 A 7 ILE A 319 VAL A 326 -1 O GLU A 324 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 ILE A 218 THR A 219 0 SHEET 2 B 4 GLY A 50 LYS A 56 1 N ASP A 55 O ILE A 218 SHEET 3 B 4 SER A 89 LEU A 96 -1 O VAL A 94 N ILE A 52 SHEET 4 B 4 ALA A 78 HIS A 80 -1 N GLY A 79 O ALA A 95 SHEET 1 C 5 ILE A 243 PRO A 245 0 SHEET 2 C 5 GLY A 50 LYS A 56 -1 N VAL A 51 O GLN A 244 SHEET 3 C 5 SER A 89 LEU A 96 -1 O VAL A 94 N ILE A 52 SHEET 4 C 5 ALA A 198 SER A 208 1 O ARG A 205 N VAL A 91 SHEET 5 C 5 PHE A 211 LYS A 212 -1 O PHE A 211 N SER A 208 SHEET 1 D11 ALA A 78 HIS A 80 0 SHEET 2 D11 SER A 89 LEU A 96 -1 O ALA A 95 N GLY A 79 SHEET 3 D11 ALA A 198 SER A 208 1 O ARG A 205 N VAL A 91 SHEET 4 D11 LYS A 111 LEU A 119 -1 N LEU A 116 O GLU A 202 SHEET 5 D11 ASP A 170 VAL A 177 -1 O VAL A 171 N MET A 117 SHEET 6 D11 THR A 155 GLU A 167 -1 N GLU A 162 O ARG A 174 SHEET 7 D11 GLY A 137 ILE A 140 -1 N ILE A 139 O ARG A 156 SHEET 8 D11 GLY C 39 PRO C 47 -1 O GLY C 46 N ILE A 140 SHEET 9 D11 TYR C 52 PRO C 57 -1 O ALA C 54 N ASP C 43 SHEET 10 D11 PHE C 15 ARG C 19 -1 N LEU C 16 O ILE C 55 SHEET 11 D11 VAL C 7 ALA C 11 -1 N ALA C 11 O PHE C 15 SHEET 1 E 3 TYR B 14 THR B 15 0 SHEET 2 E 3 ARG B 6 LYS B 7 -1 N ARG B 6 O THR B 15 SHEET 3 E 3 LYS B 28 VAL B 29 -1 O LYS B 28 N LYS B 7 SSBOND 1 CYS B 8 CYS B 23 1555 1555 2.03 SSBOND 2 CYS B 11 CYS B 23 1555 1555 2.07 LINK ZN ZN B 1 SG CYS B 8 1555 1555 2.35 LINK ZN ZN B 1 SG CYS B 11 1555 1555 2.28 LINK ZN ZN B 1 SG CYS B 23 1555 1555 2.35 SITE 1 AC1 4 CYS B 8 CYS B 11 CYS B 20 CYS B 23 CRYST1 96.561 96.561 240.978 90.00 90.00 90.00 P 41 21 2 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 0.010356 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010356 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004150 0.00000