HEADER ISOMERASE/BIOSYNTHETIC PROTEIN/RNA 03-MAY-09 3HAY TITLE CRYSTAL STRUCTURE OF A SUBSTRATE-BOUND FULL H/ACA RNP FROM PYROCOCCUS TITLE 2 FURIOSUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE TRNA PSEUDOURIDINE SYNTHASE B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE, TRNA-URIDINE COMPND 5 ISOMERASE, TRNA PSEUDOURIDYLATE SYNTHASE; COMPND 6 EC: 5.4.99.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SMALL NUCLEOLAR RNP GAR1-LIKE PROTEIN; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: GAR1; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: RIBOSOME BIOGENESIS PROTEIN NOP10; COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: 50S RIBOSOMAL PROTEIN L7AE; COMPND 19 CHAIN: D; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 5; COMPND 22 MOLECULE: H/ACA RNA; COMPND 23 CHAIN: E; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 6; COMPND 26 MOLECULE: 5'-R(*AP*UP*AP*AP*UP*UP*(FHU)P*GP*AP*CP*UP*CP*AP*A)-3'; COMPND 27 CHAIN: F; COMPND 28 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 GENE: TRUB, PF1785; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 9 ORGANISM_TAXID: 2261; SOURCE 10 GENE: PF1791; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 15 ORGANISM_TAXID: 2261; SOURCE 16 GENE: PF1141; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 MOL_ID: 4; SOURCE 20 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 21 ORGANISM_TAXID: 2261; SOURCE 22 GENE: RPL7AE, PF1367; SOURCE 23 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 25 MOL_ID: 5; SOURCE 26 SYNTHETIC: YES; SOURCE 27 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION; SOURCE 28 MOL_ID: 6; SOURCE 29 SYNTHETIC: YES KEYWDS H/ACA, GUIDE RNA, RNA-PROTEIN COMPLEX, PSEUDOURIDINE SYNTHASE, KEYWDS 2 ISOMERASE, TRNA PROCESSING, RIBONUCLEOPROTEIN, RIBOSOME BIOGENESIS, KEYWDS 3 RRNA PROCESSING, RIBOSOMAL PROTEIN, RNA-BINDING, ISOMERASE- KEYWDS 4 BIOSYNTHETIC PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.YE REVDAT 3 01-NOV-23 3HAY 1 REMARK REVDAT 2 10-NOV-21 3HAY 1 REMARK SEQADV LINK REVDAT 1 23-JUN-09 3HAY 0 JRNL AUTH J.DUAN,L.LI,J.LU,W.WANG,K.YE JRNL TITL STRUCTURAL MECHANISM OF SUBSTRATE RNA RECRUITMENT IN H/ACA JRNL TITL 2 RNA-GUIDED PSEUDOURIDINE SYNTHASE. JRNL REF MOL.CELL V. 34 427 2009 JRNL REFN ISSN 1097-2765 JRNL PMID 19481523 JRNL DOI 10.1016/J.MOLCEL.2009.05.005 REMARK 2 REMARK 2 RESOLUTION. 4.99 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12531 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) : 0.325 REMARK 3 R VALUE (WORKING SET) : 0.323 REMARK 3 FREE R VALUE : 0.367 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 654 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) : 4.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 5.11 REMARK 3 REFLECTION IN BIN (WORKING SET) : 850 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.3790 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.5090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4572 REMARK 3 NUCLEIC ACID ATOMS : 1754 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) : 263.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.06000 REMARK 3 B22 (A**2) : 10.06000 REMARK 3 B33 (A**2) : -15.09000 REMARK 3 B12 (A**2) : 5.03000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 1.323 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 1.398 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 127.599 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.891 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.873 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6634 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9361 ; 0.971 ; 2.317 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 571 ; 4.561 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 191 ;34.890 ;23.403 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 875 ;16.730 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;14.474 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1118 ; 0.055 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4283 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2456 ; 0.160 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4271 ; 0.286 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 133 ; 0.107 ; 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): 49 ; 0.173 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.095 ; 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): 2972 ; 0.185 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4664 ; 0.335 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4714 ; 0.457 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4697 ; 0.999 ; 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 : 1.40 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 3HAY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052911. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13408 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.990 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 5.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 5.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 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: 3HAX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M LITHIUM SULFATE, 50MM SODIUM REMARK 280 ACETATE (PH 4.9), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-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 93.01500 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 186.03000 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 93.01500 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 186.03000 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 93.01500 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 186.03000 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 93.01500 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 186.03000 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 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 4 REMARK 465 ALA A 5 REMARK 465 ARG A 6 REMARK 465 ASP A 7 REMARK 465 GLU A 8 REMARK 465 VAL A 9 REMARK 465 ARG A 10 REMARK 465 GLU A 338 REMARK 465 LYS A 339 REMARK 465 ARG A 340 REMARK 465 ASP A 341 REMARK 465 ARG A 342 REMARK 465 SER A 343 REMARK 465 HIS A 344 REMARK 465 HIS A 345 REMARK 465 HIS A 346 REMARK 465 HIS A 347 REMARK 465 HIS A 348 REMARK 465 HIS A 349 REMARK 465 MET B -6 REMARK 465 GLU B -5 REMARK 465 LYS B -4 REMARK 465 GLN B -3 REMARK 465 GLY B -2 REMARK 465 GLU B -1 REMARK 465 LYS B 0 REMARK 465 ARG B 75 REMARK 465 LYS B 76 REMARK 465 ARG B 77 REMARK 465 LYS B 78 REMARK 465 GLU B 79 REMARK 465 SER B 80 REMARK 465 PRO B 81 REMARK 465 LYS B 82 REMARK 465 LYS B 83 REMARK 465 ASN B 84 REMARK 465 LYS B 85 REMARK 465 GLU B 86 REMARK 465 LYS B 87 REMARK 465 ARG B 88 REMARK 465 MET B 89 REMARK 465 LYS B 90 REMARK 465 LYS B 91 REMARK 465 LYS B 92 REMARK 465 LYS B 93 REMARK 465 ARG B 94 REMARK 465 LEU B 95 REMARK 465 ASN B 96 REMARK 465 ARG B 97 REMARK 465 MET C 1 REMARK 465 LYS C 2 REMARK 465 GLY C 56 REMARK 465 ARG C 57 REMARK 465 LYS C 58 REMARK 465 GLU C 59 REMARK 465 LYS C 60 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 ALA D 3 REMARK 465 HIS D 125 REMARK 465 HIS D 126 REMARK 465 HIS D 127 REMARK 465 HIS D 128 REMARK 465 HIS D 129 REMARK 465 HIS D 130 REMARK 465 A E 62 REMARK 465 U E 63 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 G E 61 C5' C4' O4' C3' O3' C2' O2' REMARK 470 G E 61 C1' N9 C8 N7 C5 C6 O6 REMARK 470 G E 61 N1 C2 N2 N3 C4 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 A E 25 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 G E 26 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 G E 26 C3' - O3' - P ANGL. DEV. = 10.6 DEGREES REMARK 500 A E 27 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 A E 28 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 U F 6 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 G F 8 O3' - P - O5' ANGL. DEV. = 43.6 DEGREES REMARK 500 G F 8 O3' - P - OP1 ANGL. DEV. = -34.2 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 17 106.23 -54.29 REMARK 500 ARG A 19 -146.62 -79.93 REMARK 500 PHE A 49 66.15 -109.11 REMARK 500 GLU A 97 -104.84 49.87 REMARK 500 ALA A 99 20.49 -79.83 REMARK 500 PHE A 135 46.33 -86.76 REMARK 500 LEU A 164 -93.21 -76.74 REMARK 500 GLU A 213 89.54 -66.14 REMARK 500 ASP A 214 -159.53 -124.94 REMARK 500 MET A 246 -9.48 -58.28 REMARK 500 PRO A 275 5.23 -63.09 REMARK 500 ASP A 297 60.77 62.62 REMARK 500 VAL A 300 -60.28 -96.52 REMARK 500 LEU B 4 -61.75 -105.14 REMARK 500 ASN B 27 64.92 60.09 REMARK 500 ASP B 32 -154.60 -83.60 REMARK 500 PRO C 9 39.60 -93.10 REMARK 500 LYS C 10 -45.72 -154.34 REMARK 500 VAL C 22 -84.83 -107.39 REMARK 500 ASP C 39 74.46 46.90 REMARK 500 ALA D 65 -39.84 -38.86 REMARK 500 GLU D 75 -11.90 71.78 REMARK 500 PRO D 82 -75.53 -50.93 REMARK 500 ILE D 103 -71.57 -90.72 REMARK 500 MET D 123 -82.59 -77.12 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 C 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 8 SG REMARK 620 2 CYS C 11 SG 87.0 REMARK 620 3 CYS C 20 SG 115.0 118.6 REMARK 620 4 CYS C 23 SG 111.1 138.0 88.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HAX RELATED DB: PDB DBREF 3HAY A 4 343 UNP Q7LWY0 TRUB_PYRFU 1 340 DBREF 3HAY B -6 97 UNP Q8U029 Q8U029_PYRFU 1 104 DBREF 3HAY C 1 60 UNP Q8U1R4 NOP10_PYRFU 1 60 DBREF 3HAY D 3 124 UNP Q8U160 RL7A_PYRFU 2 123 DBREF 3HAY E -7 63 PDB 3HAY 3HAY -7 63 DBREF 3HAY F 1 14 PDB 3HAY 3HAY 1 14 SEQADV 3HAY HIS A 344 UNP Q7LWY0 EXPRESSION TAG SEQADV 3HAY HIS A 345 UNP Q7LWY0 EXPRESSION TAG SEQADV 3HAY HIS A 346 UNP Q7LWY0 EXPRESSION TAG SEQADV 3HAY HIS A 347 UNP Q7LWY0 EXPRESSION TAG SEQADV 3HAY HIS A 348 UNP Q7LWY0 EXPRESSION TAG SEQADV 3HAY HIS A 349 UNP Q7LWY0 EXPRESSION TAG SEQADV 3HAY LYS C 2 UNP Q8U1R4 ARG 2 ENGINEERED MUTATION SEQADV 3HAY MET D 1 UNP Q8U160 EXPRESSION TAG SEQADV 3HAY ALA D 2 UNP Q8U160 EXPRESSION TAG SEQADV 3HAY HIS D 125 UNP Q8U160 EXPRESSION TAG SEQADV 3HAY HIS D 126 UNP Q8U160 EXPRESSION TAG SEQADV 3HAY HIS D 127 UNP Q8U160 EXPRESSION TAG SEQADV 3HAY HIS D 128 UNP Q8U160 EXPRESSION TAG SEQADV 3HAY HIS D 129 UNP Q8U160 EXPRESSION TAG SEQADV 3HAY HIS D 130 UNP Q8U160 EXPRESSION TAG SEQRES 1 A 346 MET ALA ARG ASP GLU VAL ARG ARG ILE LEU PRO ALA ASP SEQRES 2 A 346 ILE LYS ARG GLU VAL LEU ILE LYS ASP GLU ASN ALA GLU SEQRES 3 A 346 THR ASN PRO ASP TRP GLY PHE PRO PRO GLU LYS ARG PRO SEQRES 4 A 346 ILE GLU MET HIS ILE GLN PHE GLY VAL ILE ASN LEU ASP SEQRES 5 A 346 LYS PRO PRO GLY PRO THR SER HIS GLU VAL VAL ALA TRP SEQRES 6 A 346 ILE LYS LYS ILE LEU ASN LEU GLU LYS ALA GLY HIS GLY SEQRES 7 A 346 GLY THR LEU ASP PRO LYS VAL SER GLY VAL LEU PRO VAL SEQRES 8 A 346 ALA LEU GLU LYS ALA THR ARG VAL VAL GLN ALA LEU LEU SEQRES 9 A 346 PRO ALA GLY LYS GLU TYR VAL ALA LEU MET HIS LEU HIS SEQRES 10 A 346 GLY ASP VAL PRO GLU ASP LYS ILE ILE GLN VAL MET LYS SEQRES 11 A 346 GLU PHE GLU GLY GLU ILE ILE GLN ARG PRO PRO LEU ARG SEQRES 12 A 346 SER ALA VAL LYS ARG ARG LEU ARG THR ARG LYS VAL TYR SEQRES 13 A 346 TYR ILE GLU VAL LEU GLU ILE GLU GLY ARG ASP VAL LEU SEQRES 14 A 346 PHE ARG VAL GLY VAL GLU ALA GLY THR TYR ILE ARG SER SEQRES 15 A 346 LEU ILE HIS HIS ILE GLY LEU ALA LEU GLY VAL GLY ALA SEQRES 16 A 346 HIS MET SER GLU LEU ARG ARG THR ARG SER GLY PRO PHE SEQRES 17 A 346 LYS GLU ASP GLU THR LEU ILE THR LEU HIS ASP LEU VAL SEQRES 18 A 346 ASP TYR TYR TYR PHE TRP LYS GLU ASP GLY ILE GLU GLU SEQRES 19 A 346 TYR PHE ARG LYS ALA ILE GLN PRO MET GLU LYS ALA VAL SEQRES 20 A 346 GLU HIS LEU PRO LYS VAL TRP ILE LYS ASP SER ALA VAL SEQRES 21 A 346 ALA ALA VAL THR HIS GLY ALA ASP LEU ALA VAL PRO GLY SEQRES 22 A 346 ILE ALA LYS LEU HIS ALA GLY ILE LYS ARG GLY ASP LEU SEQRES 23 A 346 VAL ALA ILE MET THR LEU LYS ASP GLU LEU VAL ALA LEU SEQRES 24 A 346 GLY LYS ALA MET MET THR SER GLN GLU MET LEU GLU LYS SEQRES 25 A 346 THR LYS GLY ILE ALA VAL ASP VAL GLU LYS VAL PHE MET SEQRES 26 A 346 PRO ARG ASP TRP TYR PRO LYS LEU TRP GLU LYS ARG ASP SEQRES 27 A 346 ARG SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 104 MET GLU LYS GLN GLY GLU LYS MET LYS ARG LEU GLY LYS SEQRES 2 B 104 VAL LEU HIS TYR ALA LYS GLN GLY PHE LEU ILE VAL ARG SEQRES 3 B 104 THR ASN TRP VAL PRO SER LEU ASN ASP ARG VAL VAL ASP SEQRES 4 B 104 LYS ARG LEU GLN PHE VAL GLY ILE VAL LYS ASP VAL PHE SEQRES 5 B 104 GLY PRO VAL LYS MET PRO TYR VAL ALA ILE LYS PRO LYS SEQRES 6 B 104 VAL SER ASN PRO GLU ILE TYR VAL GLY GLU VAL LEU TYR SEQRES 7 B 104 VAL ASP GLU ARG LYS ARG LYS GLU SER PRO LYS LYS ASN SEQRES 8 B 104 LYS GLU LYS ARG MET LYS LYS LYS LYS ARG LEU ASN ARG SEQRES 1 C 60 MET LYS PHE ARG ILE ARG LYS CYS PRO LYS CYS GLY ARG SEQRES 2 C 60 TYR THR LEU LYS GLU VAL CYS PRO VAL CYS GLY GLU LYS SEQRES 3 C 60 THR LYS VAL ALA HIS PRO PRO ARG PHE SER PRO GLU ASP SEQRES 4 C 60 PRO TYR GLY GLU TYR ARG ARG ARG TRP LYS ARG GLU VAL SEQRES 5 C 60 LEU GLY ILE GLY ARG LYS GLU LYS SEQRES 1 D 130 MET ALA ALA LYS PRO SER TYR VAL LYS PHE GLU VAL PRO SEQRES 2 D 130 LYS GLU LEU ALA GLU LYS ALA LEU GLN ALA VAL GLU ILE SEQRES 3 D 130 ALA ARG ASP THR GLY LYS ILE ARG LYS GLY THR ASN GLU SEQRES 4 D 130 THR THR LYS ALA VAL GLU ARG GLY GLN ALA LYS LEU VAL SEQRES 5 D 130 ILE ILE ALA GLU ASP VAL ASP PRO GLU GLU ILE VAL ALA SEQRES 6 D 130 HIS LEU PRO PRO LEU CYS GLU GLU LYS GLU ILE PRO TYR SEQRES 7 D 130 ILE TYR VAL PRO SER LYS LYS GLU LEU GLY ALA ALA ALA SEQRES 8 D 130 GLY ILE GLU VAL ALA ALA ALA SER VAL ALA ILE ILE GLU SEQRES 9 D 130 PRO GLY LYS ALA ARG ASP LEU VAL GLU GLU ILE ALA MET SEQRES 10 D 130 LYS VAL LYS GLU LEU MET LYS HIS HIS HIS HIS HIS HIS SEQRES 1 E 71 G G C U G C C U G G G U C SEQRES 2 E 71 C G C C U U G A G U G C C SEQRES 3 E 71 C G G G U G A G A A G C A SEQRES 4 E 71 U G A U C C C G G G U A A SEQRES 5 E 71 U U A U G G C G G A C C C SEQRES 6 E 71 A C A G A U SEQRES 1 F 14 A U A A U U FHU G A C U C A SEQRES 2 F 14 A MODRES 3HAY FHU F 7 U HET FHU F 7 22 HET ZN C 201 1 HETNAM FHU (5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5'- HETNAM 2 FHU MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 6 FHU C9 H14 F N2 O10 P FORMUL 7 ZN ZN 2+ HELIX 1 1 PRO A 37 ARG A 41 5 5 HELIX 2 2 GLU A 44 PHE A 49 1 6 HELIX 3 3 THR A 61 LEU A 73 1 13 HELIX 4 4 LYS A 98 LEU A 106 5 9 HELIX 5 5 PRO A 124 PHE A 135 1 12 HELIX 6 6 TYR A 182 GLY A 195 1 14 HELIX 7 7 THR A 219 GLU A 232 1 14 HELIX 8 8 ILE A 235 ALA A 242 1 8 HELIX 9 9 GLU A 247 GLU A 251 5 5 HELIX 10 10 LYS A 259 HIS A 268 1 10 HELIX 11 11 GLN A 310 LYS A 315 1 6 HELIX 12 12 TYR C 41 GLY C 54 1 14 HELIX 13 13 PRO D 13 GLY D 31 1 19 HELIX 14 14 GLY D 36 ARG D 46 1 11 HELIX 15 15 PRO D 60 VAL D 64 5 5 HELIX 16 16 HIS D 66 LYS D 74 1 9 HELIX 17 17 LYS D 84 GLY D 92 1 9 HELIX 18 18 PRO D 105 LYS D 107 5 3 HELIX 19 19 ALA D 108 LYS D 124 1 17 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 LYS A 255 O HIS A 281 SHEET 4 A 7 LEU A 289 MET A 293 1 O MET A 293 N VAL A 256 SHEET 5 A 7 LEU A 299 ALA A 305 -1 O GLY A 303 N VAL A 290 SHEET 6 A 7 ILE A 319 VAL A 326 -1 O ASP A 322 N LYS A 304 SHEET 7 A 7 LEU A 272 ALA A 273 -1 N LEU A 272 O VAL A 321 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 ALA A 198 SER A 208 1 O ARG A 205 N SER A 89 SHEET 4 B 4 PHE A 211 LYS A 212 -1 O PHE A 211 N SER A 208 SHEET 1 C 8 GLU A 138 GLN A 141 0 SHEET 2 C 8 ARG A 154 ILE A 166 -1 O ARG A 156 N ILE A 139 SHEET 3 C 8 ASP A 170 VAL A 177 -1 O LEU A 172 N GLU A 165 SHEET 4 C 8 LYS A 111 LEU A 119 -1 N LYS A 111 O VAL A 177 SHEET 5 C 8 ALA A 198 SER A 208 -1 O ARG A 204 N VAL A 114 SHEET 6 C 8 SER A 89 LEU A 96 1 N SER A 89 O ARG A 205 SHEET 7 C 8 GLY A 50 LYS A 56 -1 N LYS A 56 O GLY A 90 SHEET 8 C 8 ILE A 243 PRO A 245 -1 O GLN A 244 N VAL A 51 SHEET 1 D 6 ARG B 29 VAL B 31 0 SHEET 2 D 6 PHE B 37 PHE B 45 -1 O VAL B 38 N VAL B 30 SHEET 3 D 6 TYR B 52 PRO B 57 -1 O LYS B 56 N ILE B 40 SHEET 4 D 6 PHE B 15 ARG B 19 -1 N VAL B 18 O VAL B 53 SHEET 5 D 6 LYS B 2 ALA B 11 -1 N ALA B 11 O PHE B 15 SHEET 6 D 6 VAL B 69 VAL B 72 -1 O VAL B 72 N LYS B 2 SHEET 1 E 3 TYR C 14 THR C 15 0 SHEET 2 E 3 ARG C 6 LYS C 7 -1 N ARG C 6 O THR C 15 SHEET 3 E 3 LYS C 28 VAL C 29 -1 O LYS C 28 N LYS C 7 SHEET 1 F 4 LYS D 32 LYS D 35 0 SHEET 2 F 4 SER D 99 GLU D 104 -1 O ALA D 101 N ARG D 34 SHEET 3 F 4 LEU D 51 ALA D 55 -1 N ILE D 53 O VAL D 100 SHEET 4 F 4 TYR D 78 VAL D 81 1 O ILE D 79 N VAL D 52 LINK O3' U F 6 P FHU F 7 1555 1555 1.59 LINK O3' FHU F 7 P G F 8 1555 1555 1.59 LINK SG CYS C 8 ZN ZN C 201 1555 1555 2.36 LINK SG CYS C 11 ZN ZN C 201 1555 1555 2.36 LINK SG CYS C 20 ZN ZN C 201 1555 1555 2.36 LINK SG CYS C 23 ZN ZN C 201 1555 1555 2.35 CISPEP 1 ASP D 59 PRO D 60 0 -2.80 SITE 1 AC1 4 CYS C 8 CYS C 11 CYS C 20 CYS C 23 CRYST1 189.518 189.518 279.045 90.00 90.00 120.00 P 64 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 0.005277 0.003046 0.000000 0.00000 SCALE2 0.000000 0.006093 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003584 0.00000