HEADER ISOMERASE/RNA BINDING PROTEIN/RNA 24-FEB-10 3LWQ TITLE STRUCTURE OF H/ACA RNP BOUND TO A SUBSTRATE RNA CONTAINING 3MU 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*(UR3)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 11-AUG-10 3LWQ 1 JRNL REVDAT 1 14-JUL-10 3LWQ 0 JRNL AUTH J.ZHOU,B.LIANG,H.LI JRNL TITL FUNCTIONAL AND STRUCTURAL IMPACT OF TARGET URIDINE JRNL TITL 2 SUBSTITUTIONS ON THE H/ACA RIBONUCLEOPROTEIN PARTICLE JRNL TITL 3 PSEUDOURIDINE SYNTHASE . JRNL REF BIOCHEMISTRY V. 49 6276 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20575532 JRNL DOI 10.1021/BI1006699 REMARK 2 REMARK 2 RESOLUTION. 2.68 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) : 2.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.890 REMARK 3 COMPLETENESS FOR RANGE (%) : 45.2 REMARK 3 NUMBER OF REFLECTIONS : 25208 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1284 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 32.9768 - 5.5627 0.56 3293 162 0.2162 0.2878 REMARK 3 2 5.5627 - 4.4187 0.53 3126 178 0.1603 0.2114 REMARK 3 3 4.4187 - 3.8611 0.44 2598 155 0.1671 0.2157 REMARK 3 4 3.8611 - 3.5085 0.37 2164 131 0.2139 0.2720 REMARK 3 5 3.5085 - 3.2573 0.53 3122 156 0.2307 0.3016 REMARK 3 6 3.2573 - 3.0654 0.26 1135 61 0.3094 0.4057 REMARK 3 7 3.0654 - 2.9120 0.51 2797 139 0.2671 0.3451 REMARK 3 8 2.9120 - 2.7853 0.52 3064 164 0.2602 0.3566 REMARK 3 9 2.7853 - 2.6781 0.45 2625 138 0.2586 0.3267 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 : 0.34 REMARK 3 B_SOL : 53.25 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.970 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) : 4.45940 REMARK 3 B22 (A**2) : -17.92290 REMARK 3 B33 (A**2) : 13.46350 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 : 0.008 5622 REMARK 3 ANGLE : 1.220 7940 REMARK 3 CHIRALITY : 0.071 947 REMARK 3 PLANARITY : 0.004 747 REMARK 3 DIHEDRAL : 22.042 2441 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): 38.3395 9.6463 20.9564 REMARK 3 T TENSOR REMARK 3 T11: 0.3060 T22: 0.3549 REMARK 3 T33: 0.3072 T12: 0.0391 REMARK 3 T13: 0.0213 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 1.0398 L22: 1.5058 REMARK 3 L33: 0.6372 L12: -0.1840 REMARK 3 L13: 0.1800 L23: -0.2466 REMARK 3 S TENSOR REMARK 3 S11: -0.0991 S12: -0.1542 S13: -0.0536 REMARK 3 S21: -0.0433 S22: 0.1671 S23: 0.1924 REMARK 3 S31: 0.0719 S32: 0.0022 S33: -0.0554 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 3LWQ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-10. REMARK 100 THE RCSB ID CODE IS RCSB057825. 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 : NULL 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 : 25347 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 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 (%) : 86.6 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09300 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.63400 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 (%): 60.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 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 94.57600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.16650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 94.57600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.16650 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: 11430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 ARG A 11 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 PHE B 3 REMARK 465 ILE B 55 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 4 REMARK 465 LYS C 124 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. = 10.2 DEGREES REMARK 500 CYS B 20 CA - CB - SG ANGL. DEV. = 8.9 DEGREES REMARK 500 G D 1 O5' - C5' - C4' ANGL. DEV. = 11.4 DEGREES REMARK 500 G D 24 C3' - O3' - P ANGL. DEV. = 10.8 DEGREES REMARK 500 A D 32 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 U D 40 N1 - C1' - C2' ANGL. DEV. = 8.6 DEGREES REMARK 500 C D 41 N1 - C1' - C2' ANGL. DEV. = -10.5 DEGREES REMARK 500 U D 40 C3' - O3' - P ANGL. DEV. = 10.3 DEGREES REMARK 500 C D 56 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 G E 11 C1' - O4' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 G E 11 C3' - O3' - P ANGL. DEV. = 7.7 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 LYS A 40 -10.65 -157.91 REMARK 500 ALA A 78 121.65 166.43 REMARK 500 VAL A 91 101.69 -43.91 REMARK 500 GLU A 97 -129.62 40.87 REMARK 500 ALA A 249 -5.40 -56.47 REMARK 500 LYS A 279 132.03 -175.04 REMARK 500 LEU A 336 12.44 -65.08 REMARK 500 LYS B 10 -62.33 -104.78 REMARK 500 ASP B 39 75.39 36.55 REMARK 500 PHE C 10 158.95 174.01 REMARK 500 ALA C 27 3.75 -65.28 REMARK 500 ARG C 28 -62.35 -92.99 REMARK 500 GLU C 75 53.98 39.99 REMARK 500 ALA C 91 33.96 -143.76 REMARK 500 VAL C 95 -142.18 -95.66 REMARK 500 ALA C 108 36.28 -95.41 REMARK 500 LEU C 122 34.08 -97.51 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 61 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 11 N REMARK 620 2 CYS B 8 O 154.0 REMARK 620 3 GLY B 12 N 80.9 83.1 REMARK 620 4 LYS B 10 N 84.2 88.1 124.2 REMARK 620 5 CYS B 8 SG 89.5 116.5 129.4 103.8 REMARK 620 N 1 2 3 4 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: 3LWP RELATED DB: PDB REMARK 900 RELATED ID: 3LWR RELATED DB: PDB REMARK 900 RELATED ID: 3LWV RELATED DB: PDB DBREF 3LWQ A 4 343 UNP Q7LWY0 TRUB_PYRFU 1 340 DBREF 3LWQ B 1 60 UNP Q8U1R4 NOP10_PYRFU 1 60 DBREF 3LWQ 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 UR3 G C G G U U U MODRES 3LWQ UR3 E 10 U 3-METHYLURIDINE-5'-MONOPHOSHATE HET UR3 E 10 21 HET ZN B 61 1 HETNAM UR3 3-METHYLURIDINE-5'-MONOPHOSHATE HETNAM ZN ZINC ION FORMUL 5 UR3 C10 H15 N2 O9 P FORMUL 6 ZN ZN 2+ 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 LEU A 73 1 13 HELIX 5 5 LYS A 98 LEU A 106 5 9 HELIX 6 6 PRO A 124 LYS A 133 1 10 HELIX 7 7 TYR A 182 GLY A 195 1 14 HELIX 8 8 THR A 219 GLU A 232 1 14 HELIX 9 9 GLU A 236 ALA A 242 1 7 HELIX 10 10 GLU A 247 GLU A 251 5 5 HELIX 11 11 LYS A 259 HIS A 268 1 10 HELIX 12 12 THR A 308 LYS A 315 1 8 HELIX 13 13 TYR B 41 VAL B 52 1 12 HELIX 14 14 PRO C 13 THR C 30 1 18 HELIX 15 15 GLY C 36 GLY C 47 1 12 HELIX 16 16 PRO C 60 VAL C 64 5 5 HELIX 17 17 HIS C 66 GLU C 75 1 10 HELIX 18 18 SER C 83 ALA C 90 1 8 HELIX 19 19 ALA C 108 GLU C 121 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 LYS A 279 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 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 GLY A 137 GLN A 141 0 SHEET 2 C 8 ARG A 154 GLU A 167 -1 O VAL A 158 N GLY A 137 SHEET 3 C 8 ASP A 170 VAL A 177 -1 O GLY A 176 N TYR A 159 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 SER A 89 O ARG A 205 SHEET 7 C 8 GLY A 50 LYS A 56 -1 N LEU A 54 O LEU A 92 SHEET 8 C 8 ILE A 243 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 11 1555 1555 2.05 SSBOND 2 CYS B 8 CYS B 23 1555 1555 2.06 SSBOND 3 CYS B 8 CYS B 20 1555 1555 2.08 SSBOND 4 CYS B 11 CYS B 23 1555 1555 2.03 SSBOND 5 CYS B 11 CYS B 20 1555 1555 2.05 SSBOND 6 CYS B 20 CYS B 23 1555 1555 2.04 LINK O3' G E 9 P UR3 E 10 1555 1555 1.61 LINK O3' UR3 E 10 P G E 11 1555 1555 1.60 LINK N CYS B 11 ZN ZN B 61 1555 1555 2.07 LINK O CYS B 8 ZN ZN B 61 1555 1555 2.14 LINK N GLY B 12 ZN ZN B 61 1555 1555 2.35 LINK N LYS B 10 ZN ZN B 61 1555 1555 2.42 LINK SG CYS B 8 ZN ZN B 61 1555 1555 2.69 CISPEP 1 ASP C 59 PRO C 60 0 5.17 SITE 1 AC1 5 CYS B 8 PRO B 9 LYS B 10 CYS B 11 SITE 2 AC1 5 GLY B 12 CRYST1 189.152 64.333 84.045 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 0.005287 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015544 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011898 0.00000