HEADER HYDROLASE 05-DEC-07 3BK2 TITLE CRYSTAL STRUCTURE ANALYSIS OF THE RNASE J/UMP COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: METAL DEPENDENT HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 20-573; COMPND 5 SYNONYM: RNASE J; COMPND 6 EC: 3.-.-.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 262724; SOURCE 4 STRAIN: HB27; SOURCE 5 GENE: TTC0775; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS RNASE J, ENDORIBONUCLEASE, EXORIBONUCLEASE, METAL DEPENDENT KEYWDS 2 HYDROLASE, METALLO-BETA-LACTAMASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR I.L.DE LA SIERRA-GALLAY,L.ZIG,H.PUTZER REVDAT 6 15-NOV-23 3BK2 1 REMARK REVDAT 5 01-NOV-23 3BK2 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 3BK2 1 VERSN REVDAT 3 24-FEB-09 3BK2 1 VERSN REVDAT 2 26-FEB-08 3BK2 1 JRNL REVDAT 1 22-JAN-08 3BK2 0 JRNL AUTH I.L.DE LA SIERRA-GALLAY,L.ZIG,A.JAMALLI,H.PUTZER JRNL TITL STRUCTURAL INSIGHTS INTO THE DUAL ACTIVITY OF RNASE J JRNL REF NAT.STRUCT.MOL.BIOL. V. 15 206 2008 JRNL REFN ISSN 1545-9993 JRNL PMID 18204464 JRNL DOI 10.1038/NSMB.1376 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 38615 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 SET) : 0.217 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3869 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3430 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 625 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4304 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 14.35700 REMARK 3 B22 (A**2) : -18.11100 REMARK 3 B33 (A**2) : 3.75400 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.42 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.40 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.315 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 55.66 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : LIGAND_XPLOR_PAR.TXT REMARK 3 PARAMETER FILE 4 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 5 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3BK2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38615 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.43100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.970 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 3BK1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-4% PEG 4K, 0.02M AMMONIUM SULFATE, REMARK 280 0.1M NA-MES, THE RNASE J/UMP COMPLEX WAS OBTAINED BY SOAKING OF REMARK 280 A NATIVE RNASE J CRYSTAL IN 100MM UMP, PH5.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: F 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z+1/2 REMARK 290 7555 -X,Y+1/2,-Z+1/2 REMARK 290 8555 X,-Y+1/2,-Z+1/2 REMARK 290 9555 X+1/2,Y,Z+1/2 REMARK 290 10555 -X+1/2,-Y,Z+1/2 REMARK 290 11555 -X+1/2,Y,-Z+1/2 REMARK 290 12555 X+1/2,-Y,-Z+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z REMARK 290 14555 -X+1/2,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y+1/2,-Z REMARK 290 16555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 114.16000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 114.16000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 59.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 114.16000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 59.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 114.16000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 49.04000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 114.16000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 49.04000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 114.16000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 49.04000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 114.16000 REMARK 290 SMTRY1 12 1.000000 0.000000 0.000000 49.04000 REMARK 290 SMTRY2 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 114.16000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 49.04000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 59.00000 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 49.04000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 59.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 49.04000 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 59.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 49.04000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 59.00000 REMARK 290 SMTRY3 16 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8520 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 49.04000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 59.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 993 LIES ON A SPECIAL POSITION. 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 -6 REMARK 465 SER A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 SER A 2 REMARK 465 GLN A 3 REMARK 465 GLY A 4 REMARK 465 GLY A 5 REMARK 465 PRO A 6 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 ARG A 120 CG CD NE CZ NH1 NH2 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 23 54.23 35.14 REMARK 500 ARG A 31 -112.98 53.02 REMARK 500 ASP A 38 170.11 67.33 REMARK 500 MSE A 48 57.92 -113.32 REMARK 500 ARG A 120 161.65 -47.51 REMARK 500 PRO A 121 -77.89 -60.02 REMARK 500 LEU A 175 74.97 -109.85 REMARK 500 ASP A 285 -112.06 -92.97 REMARK 500 ASP A 295 43.13 -98.32 REMARK 500 PHE A 321 -96.57 -121.84 REMARK 500 SER A 338 51.43 -98.66 REMARK 500 THR A 390 64.11 32.70 REMARK 500 LEU A 453 28.24 -70.67 REMARK 500 LYS A 520 18.22 59.51 REMARK 500 ASP A 545 67.07 -117.53 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 A 948 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 75 NE2 REMARK 620 2 HIS A 77 ND1 98.7 REMARK 620 3 HIS A 150 NE2 106.3 93.2 REMARK 620 4 ASP A 172 OD2 91.3 168.1 90.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 949 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 79 OD2 REMARK 620 2 HIS A 80 NE2 90.0 REMARK 620 3 ASP A 172 OD2 166.6 92.0 REMARK 620 4 HIS A 398 NE2 100.2 107.3 91.8 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 SO4 A 947 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 948 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 949 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P A 950 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BK1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FREE RNASE J DBREF 3BK2 A 2 555 UNP Q72JJ7 Q72JJ7_THET2 20 573 SEQADV 3BK2 MET A -6 UNP Q72JJ7 EXPRESSION TAG SEQADV 3BK2 SER A -5 UNP Q72JJ7 EXPRESSION TAG SEQADV 3BK2 HIS A -4 UNP Q72JJ7 EXPRESSION TAG SEQADV 3BK2 HIS A -3 UNP Q72JJ7 EXPRESSION TAG SEQADV 3BK2 HIS A -2 UNP Q72JJ7 EXPRESSION TAG SEQADV 3BK2 HIS A -1 UNP Q72JJ7 EXPRESSION TAG SEQADV 3BK2 HIS A 0 UNP Q72JJ7 EXPRESSION TAG SEQADV 3BK2 HIS A 1 UNP Q72JJ7 EXPRESSION TAG SEQRES 1 A 562 MET SER HIS HIS HIS HIS HIS HIS SER GLN GLY GLY PRO SEQRES 2 A 562 GLN ASP HIS VAL GLU ILE ILE PRO LEU GLY GLY MSE GLY SEQRES 3 A 562 GLU ILE GLY LYS ASN ILE THR VAL PHE ARG PHE ARG ASP SEQRES 4 A 562 GLU ILE PHE VAL LEU ASP GLY GLY LEU ALA PHE PRO GLU SEQRES 5 A 562 GLU GLY MSE PRO GLY VAL ASP LEU LEU ILE PRO ARG VAL SEQRES 6 A 562 ASP TYR LEU ILE GLU HIS ARG HIS LYS ILE LYS ALA TRP SEQRES 7 A 562 VAL LEU THR HIS GLY HIS GLU ASP HIS ILE GLY GLY LEU SEQRES 8 A 562 PRO PHE LEU LEU PRO MSE ILE PHE GLY LYS GLU SER PRO SEQRES 9 A 562 VAL PRO ILE TYR GLY ALA ARG LEU THR LEU GLY LEU LEU SEQRES 10 A 562 ARG GLY LYS LEU GLU GLU PHE GLY LEU ARG PRO GLY ALA SEQRES 11 A 562 PHE ASN LEU LYS GLU ILE SER PRO ASP ASP ARG ILE GLN SEQRES 12 A 562 VAL GLY ARG TYR PHE THR LEU ASP LEU PHE ARG MSE THR SEQRES 13 A 562 HIS SER ILE PRO ASP ASN SER GLY VAL VAL ILE ARG THR SEQRES 14 A 562 PRO ILE GLY THR ILE VAL HIS THR GLY ASP PHE LYS LEU SEQRES 15 A 562 ASP PRO THR PRO ILE ASP GLY LYS VAL SER HIS LEU ALA SEQRES 16 A 562 LYS VAL ALA GLN ALA GLY ALA GLU GLY VAL LEU LEU LEU SEQRES 17 A 562 ILE ALA ASP ALA THR ASN ALA GLU ARG PRO GLY TYR THR SEQRES 18 A 562 PRO SER GLU MSE GLU ILE ALA LYS GLU LEU ASP ARG VAL SEQRES 19 A 562 ILE GLY ARG ALA PRO GLY ARG VAL PHE VAL THR THR PHE SEQRES 20 A 562 ALA SER HIS ILE HIS ARG ILE GLN SER VAL ILE TRP ALA SEQRES 21 A 562 ALA GLU LYS TYR GLY ARG LYS VAL ALA MSE GLU GLY ARG SEQRES 22 A 562 SER MSE LEU LYS PHE SER ARG ILE ALA LEU GLU LEU GLY SEQRES 23 A 562 TYR LEU LYS VAL LYS ASP ARG LEU TYR THR LEU GLU GLU SEQRES 24 A 562 VAL LYS ASP LEU PRO ASP HIS GLN VAL LEU ILE LEU ALA SEQRES 25 A 562 THR GLY SER GLN GLY GLN PRO MSE SER VAL LEU HIS ARG SEQRES 26 A 562 LEU ALA PHE GLU GLY HIS ALA LYS MSE ALA ILE LYS PRO SEQRES 27 A 562 GLY ASP THR VAL ILE LEU SER SER SER PRO ILE PRO GLY SEQRES 28 A 562 ASN GLU GLU ALA VAL ASN ARG VAL ILE ASN ARG LEU TYR SEQRES 29 A 562 ALA LEU GLY ALA TYR VAL LEU TYR PRO PRO THR TYR LYS SEQRES 30 A 562 VAL HIS ALA SER GLY HIS ALA SER GLN GLU GLU LEU LYS SEQRES 31 A 562 LEU ILE LEU ASN LEU THR THR PRO ARG PHE PHE LEU PRO SEQRES 32 A 562 TRP HIS GLY GLU VAL ARG HIS GLN MSE ASN PHE LYS TRP SEQRES 33 A 562 LEU ALA GLU SER MSE SER ARG PRO PRO GLU LYS THR LEU SEQRES 34 A 562 ILE GLY GLU ASN GLY ALA VAL TYR ARG LEU THR ARG GLU SEQRES 35 A 562 THR PHE GLU LYS VAL GLY GLU VAL PRO HIS GLY VAL LEU SEQRES 36 A 562 TYR VAL ASP GLY LEU GLY VAL GLY ASP ILE THR GLU GLU SEQRES 37 A 562 ILE LEU ALA ASP ARG ARG HIS MSE ALA GLU GLU GLY LEU SEQRES 38 A 562 VAL VAL ILE THR ALA LEU ALA GLY GLU ASP PRO VAL VAL SEQRES 39 A 562 GLU VAL VAL SER ARG GLY PHE VAL LYS ALA GLY GLU ARG SEQRES 40 A 562 LEU LEU GLY GLU VAL ARG ARG MSE ALA LEU GLU ALA LEU SEQRES 41 A 562 LYS ASN GLY VAL ARG GLU LYS LYS PRO LEU GLU ARG ILE SEQRES 42 A 562 ARG ASP ASP ILE TYR TYR PRO VAL LYS LYS PHE LEU LYS SEQRES 43 A 562 LYS ALA THR GLY ARG ASP PRO MSE ILE LEU PRO VAL VAL SEQRES 44 A 562 ILE GLU GLY MODRES 3BK2 MSE A 18 MET SELENOMETHIONINE MODRES 3BK2 MSE A 48 MET SELENOMETHIONINE MODRES 3BK2 MSE A 90 MET SELENOMETHIONINE MODRES 3BK2 MSE A 148 MET SELENOMETHIONINE MODRES 3BK2 MSE A 218 MET SELENOMETHIONINE MODRES 3BK2 MSE A 263 MET SELENOMETHIONINE MODRES 3BK2 MSE A 268 MET SELENOMETHIONINE MODRES 3BK2 MSE A 313 MET SELENOMETHIONINE MODRES 3BK2 MSE A 327 MET SELENOMETHIONINE MODRES 3BK2 MSE A 405 MET SELENOMETHIONINE MODRES 3BK2 MSE A 414 MET SELENOMETHIONINE MODRES 3BK2 MSE A 469 MET SELENOMETHIONINE MODRES 3BK2 MSE A 508 MET SELENOMETHIONINE MODRES 3BK2 MSE A 547 MET SELENOMETHIONINE HET MSE A 18 8 HET MSE A 48 8 HET MSE A 90 8 HET MSE A 148 8 HET MSE A 218 8 HET MSE A 263 8 HET MSE A 268 8 HET MSE A 313 8 HET MSE A 327 8 HET MSE A 405 8 HET MSE A 414 8 HET MSE A 469 8 HET MSE A 508 8 HET MSE A 547 8 HET SO4 A 947 5 HET ZN A 948 1 HET ZN A 949 1 HET U5P A 950 21 HET GOL A 601 6 HET GOL A 602 6 HET GOL A 603 6 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION HETNAM U5P URIDINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 14(C5 H11 N O2 SE) FORMUL 2 SO4 O4 S 2- FORMUL 3 ZN 2(ZN 2+) FORMUL 5 U5P C9 H13 N2 O9 P FORMUL 6 GOL 3(C3 H8 O3) FORMUL 9 HOH *175(H2 O) HELIX 1 1 VAL A 58 HIS A 64 1 7 HELIX 2 2 HIS A 77 GLY A 82 1 6 HELIX 3 3 GLY A 83 GLY A 93 1 11 HELIX 4 4 ARG A 104 PHE A 117 1 14 HELIX 5 5 LEU A 187 GLY A 197 1 11 HELIX 6 6 SER A 216 ALA A 231 1 16 HELIX 7 7 HIS A 243 TYR A 257 1 15 HELIX 8 8 GLY A 265 LEU A 278 1 14 HELIX 9 9 LEU A 290 LYS A 294 5 5 HELIX 10 10 PRO A 297 HIS A 299 5 3 HELIX 11 11 PRO A 312 PHE A 321 1 10 HELIX 12 12 ASN A 345 LEU A 359 1 15 HELIX 13 13 SER A 378 THR A 390 1 13 HELIX 14 14 GLU A 400 SER A 413 1 14 HELIX 15 15 THR A 459 GLY A 473 1 15 HELIX 16 16 VAL A 495 ARG A 500 1 6 HELIX 17 17 LEU A 501 GLU A 519 1 19 HELIX 18 18 PRO A 522 GLY A 543 1 22 SHEET 1 A 8 ASN A 125 ILE A 129 0 SHEET 2 A 8 PRO A 99 ALA A 103 1 N ILE A 100 O LYS A 127 SHEET 3 A 8 ILE A 68 VAL A 72 1 N TRP A 71 O PRO A 99 SHEET 4 A 8 GLU A 33 LEU A 37 1 N ILE A 34 O LYS A 69 SHEET 5 A 8 ILE A 25 PHE A 30 -1 N THR A 26 O LEU A 37 SHEET 6 A 8 VAL A 10 GLY A 16 -1 N ILE A 13 O VAL A 27 SHEET 7 A 8 ALA A 428 LEU A 432 -1 O LEU A 432 N VAL A 10 SHEET 8 A 8 PHE A 437 GLU A 442 -1 O VAL A 440 N VAL A 429 SHEET 1 B 3 LEU A 53 PRO A 56 0 SHEET 2 B 3 VAL A 447 ASP A 451 -1 O VAL A 450 N LEU A 53 SHEET 3 B 3 GLY A 454 ILE A 458 -1 O GLY A 456 N TYR A 449 SHEET 1 C 7 ARG A 134 VAL A 137 0 SHEET 2 C 7 PHE A 141 ARG A 147 -1 O PHE A 141 N VAL A 137 SHEET 3 C 7 SER A 156 THR A 162 -1 O VAL A 159 N ASP A 144 SHEET 4 C 7 GLY A 165 HIS A 169 -1 O ILE A 167 N ILE A 160 SHEET 5 C 7 LEU A 200 ASP A 204 1 O LEU A 200 N VAL A 168 SHEET 6 C 7 PHE A 393 TRP A 397 1 O LEU A 395 N LEU A 201 SHEET 7 C 7 LYS A 420 THR A 421 1 O LYS A 420 N PHE A 394 SHEET 1 D 5 LYS A 260 GLU A 264 0 SHEET 2 D 5 VAL A 301 ALA A 305 1 O LEU A 304 N ALA A 262 SHEET 3 D 5 VAL A 235 THR A 238 1 N VAL A 237 O ILE A 303 SHEET 4 D 5 THR A 334 LEU A 337 1 O ILE A 336 N PHE A 236 SHEET 5 D 5 TYR A 362 LEU A 364 1 O LEU A 364 N VAL A 335 SHEET 1 E 3 VAL A 486 ARG A 492 0 SHEET 2 E 3 LEU A 474 ALA A 481 -1 N THR A 478 O GLU A 488 SHEET 3 E 3 MSE A 547 GLU A 554 1 O MSE A 547 N VAL A 475 LINK C GLY A 17 N MSE A 18 1555 1555 1.33 LINK C MSE A 18 N GLY A 19 1555 1555 1.33 LINK C GLY A 47 N MSE A 48 1555 1555 1.33 LINK C MSE A 48 N PRO A 49 1555 1555 1.35 LINK C PRO A 89 N MSE A 90 1555 1555 1.33 LINK C MSE A 90 N ILE A 91 1555 1555 1.33 LINK C ARG A 147 N MSE A 148 1555 1555 1.33 LINK C MSE A 148 N THR A 149 1555 1555 1.33 LINK C GLU A 217 N MSE A 218 1555 1555 1.33 LINK C MSE A 218 N GLU A 219 1555 1555 1.33 LINK C ALA A 262 N MSE A 263 1555 1555 1.33 LINK C MSE A 263 N GLU A 264 1555 1555 1.33 LINK C SER A 267 N MSE A 268 1555 1555 1.33 LINK C MSE A 268 N LEU A 269 1555 1555 1.33 LINK C PRO A 312 N MSE A 313 1555 1555 1.33 LINK C MSE A 313 N SER A 314 1555 1555 1.33 LINK C LYS A 326 N MSE A 327 1555 1555 1.33 LINK C MSE A 327 N ALA A 328 1555 1555 1.33 LINK C GLN A 404 N MSE A 405 1555 1555 1.33 LINK C MSE A 405 N ASN A 406 1555 1555 1.33 LINK C SER A 413 N MSE A 414 1555 1555 1.34 LINK C MSE A 414 N SER A 415 1555 1555 1.33 LINK C HIS A 468 N MSE A 469 1555 1555 1.33 LINK C MSE A 469 N ALA A 470 1555 1555 1.33 LINK C ARG A 507 N MSE A 508 1555 1555 1.33 LINK C MSE A 508 N ALA A 509 1555 1555 1.33 LINK C PRO A 546 N MSE A 547 1555 1555 1.33 LINK C MSE A 547 N ILE A 548 1555 1555 1.33 LINK NE2 HIS A 75 ZN ZN A 948 1555 1555 2.36 LINK ND1 HIS A 77 ZN ZN A 948 1555 1555 2.22 LINK OD2 ASP A 79 ZN ZN A 949 1555 1555 2.37 LINK NE2 HIS A 80 ZN ZN A 949 1555 1555 2.25 LINK NE2 HIS A 150 ZN ZN A 948 1555 1555 2.22 LINK OD2 ASP A 172 ZN ZN A 948 1555 1555 2.37 LINK OD2 ASP A 172 ZN ZN A 949 1555 1555 2.18 LINK NE2 HIS A 398 ZN ZN A 949 1555 1555 2.26 CISPEP 1 PRO A 366 PRO A 367 0 0.39 SITE 1 AC1 4 ARG A 147 HIS A 186 ARG A 416 GOL A 603 SITE 1 AC2 5 HIS A 75 HIS A 77 HIS A 150 ASP A 172 SITE 2 AC2 5 ZN A 949 SITE 1 AC3 5 ASP A 79 HIS A 80 ASP A 172 HIS A 398 SITE 2 AC3 5 ZN A 948 SITE 1 AC4 17 ILE A 21 GLU A 78 ASP A 79 PHE A 240 SITE 2 AC4 17 HIS A 243 SER A 340 PRO A 341 ILE A 342 SITE 3 AC4 17 PRO A 343 HIS A 372 SER A 374 GLY A 375 SITE 4 AC4 17 HIS A 376 HOH A 957 HOH A 964 HOH A1103 SITE 5 AC4 17 HOH A1116 SITE 1 AC5 2 GLN A 379 ASN A 406 SITE 1 AC6 4 LYS A 222 ASP A 225 TRP A 252 HOH A1107 SITE 1 AC7 5 HIS A 186 ALA A 195 SO4 A 947 HOH A1061 SITE 2 AC7 5 HOH A1101 CRYST1 98.080 118.000 228.320 90.00 90.00 90.00 F 2 2 2 16 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 0.010196 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008475 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004380 0.00000