HEADER ISOMERASE/RNA BINDING PROTEIN/RNA 24-FEB-10 3LWP TITLE STRUCTURE OF H/ACA RNP BOUND TO A SUBSTRATE RNA CONTAINING 5BRDU COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSEUDOURIDINE SYNTHASE CBF5; 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: RIBOSOME BIOGENESIS PROTEIN NOP10; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 50S RIBOSOMAL PROTEIN L7AE; COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: H/ACA RNA; COMPND 18 CHAIN: D; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 5; COMPND 21 MOLECULE: 5'-R(*GP*AP*GP*CP*GP*(BRU)P*GP*CP*GP*GP*UP*UP*U)-3; COMPND 22 CHAIN: E; COMPND 23 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: PF1141; 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: PF1367, RPL7AE; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 OTHER_DETAILS: IN VITRO TRANSCRIPTION; SOURCE 22 MOL_ID: 5; SOURCE 23 SYNTHETIC: YES; SOURCE 24 OTHER_DETAILS: COMMERCIAL SOURCE KEYWDS H/ACA PSEUDOURIDINE SYNTHASE, ISOMERASE, TRNA PROCESSING, KEYWDS 2 RIBONUCLEOPROTEIN, RIBOSOME BIOGENESIS, RRNA PROCESSING, RIBOSOMAL KEYWDS 3 PROTEIN, RNA-BINDING, ISOMERASE-RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHOU,B.LIANG,C.LV,W.YANG,H.LI REVDAT 2 01-SEP-10 3LWP 1 JRNL REVDAT 1 14-JUL-10 3LWP 0 JRNL AUTH J.ZHOU,C.LV,B.LIANG,M.CHEN,W.YANG,H.LI JRNL TITL GLYCOSIDIC BOND CONFORMATION PREFERENCE PLAYS A PIVOTAL ROLE JRNL TITL 2 IN CATALYSIS OF RNA PSEUDOURIDYLATION: A COMBINED SIMULATION JRNL TITL 3 AND STRUCTURAL STUDY. JRNL REF J.MOL.BIOL. V. 401 690 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20615421 JRNL DOI 10.1016/J.JMB.2010.06.061 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.890 REMARK 3 COMPLETENESS FOR RANGE (%) : 51.4 REMARK 3 NUMBER OF REFLECTIONS : 35135 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1750 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.8442 - 5.7138 0.56 3039 158 0.1995 0.2258 REMARK 3 2 5.7138 - 4.5384 0.53 2855 155 0.1532 0.2052 REMARK 3 3 4.5384 - 3.9656 0.51 2759 141 0.1449 0.2043 REMARK 3 4 3.9656 - 3.6034 0.48 2621 136 0.1697 0.2206 REMARK 3 5 3.6034 - 3.3454 0.52 2837 147 0.1848 0.2289 REMARK 3 6 3.3454 - 3.1483 0.50 2709 144 0.2144 0.2845 REMARK 3 7 3.1483 - 2.9907 0.47 2521 154 0.2520 0.3336 REMARK 3 8 2.9907 - 2.8606 0.52 2824 148 0.2492 0.3114 REMARK 3 9 2.8606 - 2.7505 0.52 2836 152 0.2623 0.2955 REMARK 3 10 2.7505 - 2.6556 0.52 2826 131 0.2607 0.3692 REMARK 3 11 2.6556 - 2.5726 0.52 2779 146 0.2828 0.3355 REMARK 3 12 2.5726 - 2.4500 0.51 2779 138 0.2993 0.3775 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 35.55 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.630 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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) : 8.91820 REMARK 3 B22 (A**2) : -7.67350 REMARK 3 B33 (A**2) : -1.24470 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 5660 REMARK 3 ANGLE : 1.428 7989 REMARK 3 CHIRALITY : 0.080 951 REMARK 3 PLANARITY : 0.006 753 REMARK 3 DIHEDRAL : 22.949 2477 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 38.2039 9.5072 20.8992 REMARK 3 T TENSOR REMARK 3 T11: 0.1540 T22: 0.1716 REMARK 3 T33: 0.1319 T12: 0.0760 REMARK 3 T13: 0.0246 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 0.2847 L22: 0.9100 REMARK 3 L33: 0.1620 L12: 0.0732 REMARK 3 L13: 0.0456 L23: -0.1712 REMARK 3 S TENSOR REMARK 3 S11: -0.0478 S12: -0.0677 S13: 0.0117 REMARK 3 S21: -0.0715 S22: 0.0824 S23: 0.1738 REMARK 3 S31: -0.0383 S32: 0.0720 S33: -0.0328 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3LWP COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-10. REMARK 100 THE RCSB ID CODE IS RCSB057824. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35248 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.56000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP. VAPOR REMARK 280 DIFFUSION, HANGING DROP. VAPOR DIFFUSION, HANGING DROP. VAPOR REMARK 280 DIFFUSION, HANGING DROP. VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 94.08650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 94.08650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.29000 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, B, C, 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 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 PRO A 143 REMARK 465 PRO A 144 REMARK 465 LEU A 145 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 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 MET B 1 REMARK 465 ARG B 2 REMARK 465 GLY B 56 REMARK 465 ARG B 57 REMARK 465 LYS B 58 REMARK 465 GLU B 59 REMARK 465 LYS B 60 REMARK 465 MET C 2 REMARK 465 ALA C 3 REMARK 465 LYS C 124 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 CYS B 20 CB CYS B 20 SG 0.125 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 CYS B 8 CA - CB - SG ANGL. DEV. = 10.8 DEGREES REMARK 500 CYS B 20 CA - CB - SG ANGL. DEV. = 14.3 DEGREES REMARK 500 G D 1 O5' - C5' - C4' ANGL. DEV. = 14.3 DEGREES REMARK 500 G D 19 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 G D 24 C3' - O3' - P ANGL. DEV. = 12.2 DEGREES REMARK 500 U D 26 O4' - C1' - N1 ANGL. DEV. = -6.2 DEGREES REMARK 500 A D 25 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 C D 27 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 U D 40 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 C D 41 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 C D 45 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 C D 56 C6 - N1 - C2 ANGL. DEV. = 3.0 DEGREES REMARK 500 C D 56 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 G E 9 O4' - C1' - N9 ANGL. DEV. = 6.3 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 PRO A 32 1.14 -63.63 REMARK 500 PRO A 38 -57.22 -27.63 REMARK 500 GLU A 39 38.61 -93.36 REMARK 500 ALA A 78 147.44 -173.80 REMARK 500 GLU A 97 -117.07 37.86 REMARK 500 GLN A 104 -7.32 -56.43 REMARK 500 ASP A 214 -163.80 -110.12 REMARK 500 ALA A 249 7.29 -63.20 REMARK 500 ASP C 57 40.38 -104.64 REMARK 500 PRO C 105 -75.32 -61.74 REMARK 500 LYS C 107 -5.14 -58.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LYS B 7 24.7 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL 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 61 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LWO RELATED DB: PDB REMARK 900 RELATED ID: 3LWQ RELATED DB: PDB REMARK 900 RELATED ID: 3LWR RELATED DB: PDB REMARK 900 RELATED ID: 3LWV RELATED DB: PDB DBREF 3LWP A 4 343 UNP Q7LWY0 TRUB_PYRFU 1 340 DBREF 3LWP B 1 60 UNP Q8U1R4 NOP10_PYRFU 1 60 DBREF 3LWP C 2 124 UNP Q8U160 RL7A_PYRFU 1 123 SEQRES 1 A 340 MET ALA ARG ASP GLU VAL ARG ARG ILE LEU PRO ALA ASP SEQRES 2 A 340 ILE LYS ARG GLU VAL LEU ILE LYS ASP GLU ASN ALA GLU SEQRES 3 A 340 THR ASN PRO ASP TRP GLY PHE PRO PRO GLU LYS ARG PRO SEQRES 4 A 340 ILE GLU MET HIS ILE GLN PHE GLY VAL ILE ASN LEU ASP SEQRES 5 A 340 LYS PRO PRO GLY PRO THR SER HIS GLU VAL VAL ALA TRP SEQRES 6 A 340 ILE LYS LYS ILE LEU ASN LEU GLU LYS ALA GLY HIS GLY SEQRES 7 A 340 GLY THR LEU ASP PRO LYS VAL SER GLY VAL LEU PRO VAL SEQRES 8 A 340 ALA LEU GLU LYS ALA THR ARG VAL VAL GLN ALA LEU LEU SEQRES 9 A 340 PRO ALA GLY LYS GLU TYR VAL ALA LEU MET HIS LEU HIS SEQRES 10 A 340 GLY ASP VAL PRO GLU ASP LYS ILE ILE GLN VAL MET LYS SEQRES 11 A 340 GLU PHE GLU GLY GLU ILE ILE GLN ARG PRO PRO LEU ARG SEQRES 12 A 340 SER ALA VAL LYS ARG ARG LEU ARG THR ARG LYS VAL TYR SEQRES 13 A 340 TYR ILE GLU VAL LEU GLU ILE GLU GLY ARG ASP VAL LEU SEQRES 14 A 340 PHE ARG VAL GLY VAL GLU ALA GLY THR TYR ILE ARG SER SEQRES 15 A 340 LEU ILE HIS HIS ILE GLY LEU ALA LEU GLY VAL GLY ALA SEQRES 16 A 340 HIS MET SER GLU LEU ARG ARG THR ARG SER GLY PRO PHE SEQRES 17 A 340 LYS GLU ASP GLU THR LEU ILE THR LEU HIS ASP LEU VAL SEQRES 18 A 340 ASP TYR TYR TYR PHE TRP LYS GLU ASP GLY ILE GLU GLU SEQRES 19 A 340 TYR PHE ARG LYS ALA ILE GLN PRO MET GLU LYS ALA VAL SEQRES 20 A 340 GLU HIS LEU PRO LYS VAL TRP ILE LYS ASP SER ALA VAL SEQRES 21 A 340 ALA ALA VAL THR HIS GLY ALA ASP LEU ALA VAL PRO GLY SEQRES 22 A 340 ILE ALA LYS LEU HIS ALA GLY ILE LYS ARG GLY ASP LEU SEQRES 23 A 340 VAL ALA ILE MET THR LEU LYS ASP GLU LEU VAL ALA LEU SEQRES 24 A 340 GLY LYS ALA MET MET THR SER GLN GLU MET LEU GLU LYS SEQRES 25 A 340 THR LYS GLY ILE ALA VAL ASP VAL GLU LYS VAL PHE MET SEQRES 26 A 340 PRO ARG ASP TRP TYR PRO LYS LEU TRP GLU LYS ARG ASP SEQRES 27 A 340 ARG SER SEQRES 1 B 60 MET ARG PHE ARG ILE ARG LYS CYS PRO LYS CYS GLY ARG SEQRES 2 B 60 TYR THR LEU LYS GLU VAL CYS PRO VAL CYS GLY GLU LYS SEQRES 3 B 60 THR LYS VAL ALA HIS PRO PRO ARG PHE SER PRO GLU ASP SEQRES 4 B 60 PRO TYR GLY GLU TYR ARG ARG ARG TRP LYS ARG GLU VAL SEQRES 5 B 60 LEU GLY ILE GLY ARG LYS GLU LYS SEQRES 1 C 123 MET ALA LYS PRO SER TYR VAL LYS PHE GLU VAL PRO LYS SEQRES 2 C 123 GLU LEU ALA GLU LYS ALA LEU GLN ALA VAL GLU ILE ALA SEQRES 3 C 123 ARG ASP THR GLY LYS ILE ARG LYS GLY THR ASN GLU THR SEQRES 4 C 123 THR LYS ALA VAL GLU ARG GLY GLN ALA LYS LEU VAL ILE SEQRES 5 C 123 ILE ALA GLU ASP VAL ASP PRO GLU GLU ILE VAL ALA HIS SEQRES 6 C 123 LEU PRO PRO LEU CYS GLU GLU LYS GLU ILE PRO TYR ILE SEQRES 7 C 123 TYR VAL PRO SER LYS LYS GLU LEU GLY ALA ALA ALA GLY SEQRES 8 C 123 ILE GLU VAL ALA ALA ALA SER VAL ALA ILE ILE GLU PRO SEQRES 9 C 123 GLY LYS ALA ARG ASP LEU VAL GLU GLU ILE ALA MET LYS SEQRES 10 C 123 VAL LYS GLU LEU MET LYS SEQRES 1 D 58 G G G C C A C G G A A A C SEQRES 2 D 58 C G C G C G C G G U G A U SEQRES 3 D 58 C A A U G A G C C G C G U SEQRES 4 D 58 U C G C U C C C G U G G C SEQRES 5 D 58 C C A C A A SEQRES 1 E 13 G A G C G BRU G C G G U U U MODRES 3LWP BRU E 10 DU HET BRU E 10 20 HET ZN B 61 1 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 5 BRU C9 H12 BR N2 O8 P FORMUL 6 ZN ZN 2+ FORMUL 7 HOH *28(H2 O) HELIX 1 1 LEU A 13 ILE A 17 5 5 HELIX 2 2 PRO A 37 ARG A 41 5 5 HELIX 3 3 PRO A 42 PHE A 49 1 8 HELIX 4 4 THR A 61 ASN A 74 1 14 HELIX 5 5 LYS A 98 ARG A 101 5 4 HELIX 6 6 VAL A 102 LEU A 107 1 6 HELIX 7 7 PRO A 124 LYS A 133 1 10 HELIX 8 8 TYR A 182 LEU A 194 1 13 HELIX 9 9 THR A 219 GLU A 232 1 14 HELIX 10 10 GLU A 236 ILE A 243 1 8 HELIX 11 11 GLU A 247 GLU A 251 5 5 HELIX 12 12 LYS A 259 HIS A 268 1 10 HELIX 13 13 THR A 308 LYS A 315 1 8 HELIX 14 14 TYR B 41 GLY B 54 1 14 HELIX 15 15 PRO C 13 GLY C 31 1 19 HELIX 16 16 GLY C 36 ARG C 46 1 11 HELIX 17 17 PRO C 60 VAL C 64 5 5 HELIX 18 18 HIS C 66 LYS C 74 1 9 HELIX 19 19 SER C 83 ALA C 91 1 9 HELIX 20 20 ALA C 108 MET C 123 1 16 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 THR A 294 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 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 ALA A 198 SER A 208 1 O ARG A 205 N VAL A 91 SHEET 4 B 4 PHE A 211 LYS A 212 -1 O PHE A 211 N SER A 208 SHEET 1 C 8 GLY A 137 GLN A 141 0 SHEET 2 C 8 ARG A 154 GLU A 167 -1 O ARG A 154 N GLN A 141 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 GLU A 202 N LEU A 116 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 GLY A 50 O LEU A 96 SHEET 8 C 8 GLN A 244 PRO A 245 -1 O GLN A 244 N VAL A 51 SHEET 1 D 3 TYR B 14 THR B 15 0 SHEET 2 D 3 ARG B 6 LYS B 7 -1 N ARG B 6 O THR B 15 SHEET 3 D 3 LYS B 28 VAL B 29 -1 O LYS B 28 N LYS B 7 SHEET 1 E 4 LYS C 32 LYS C 35 0 SHEET 2 E 4 SER C 99 GLU C 104 -1 O GLU C 104 N LYS C 32 SHEET 3 E 4 LEU C 51 ALA C 55 -1 N ILE C 53 O VAL C 100 SHEET 4 E 4 TYR C 78 VAL C 81 1 O ILE C 79 N ILE C 54 SSBOND 1 CYS B 8 CYS B 23 1555 1555 2.06 SSBOND 2 CYS B 8 CYS B 11 1555 1555 2.07 SSBOND 3 CYS B 8 CYS B 20 1555 1555 2.16 SSBOND 4 CYS B 11 CYS B 23 1555 1555 2.00 SSBOND 5 CYS B 11 CYS B 20 1555 1555 2.05 SSBOND 6 CYS B 20 CYS B 23 1555 1555 2.06 LINK O3' G E 9 P BRU E 10 1555 1555 1.61 LINK O3' BRU E 10 P G E 11 1555 1555 1.61 CISPEP 1 ASP C 59 PRO C 60 0 8.13 SITE 1 AC1 4 GLY A 195 VAL A 196 CYS B 11 VAL B 22 CRYST1 188.173 64.580 83.798 90.00 90.00 90.00 P 21 21 2 4 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 0.005314 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015485 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011933 0.00000