HEADER HYDROLASE/RNA 25-JUL-11 3T3N TITLE MOLECULAR BASIS FOR THE RECOGNITION AND CLEAVAGE OF RNA (UUCCGU) BY TITLE 2 THE BIFUNCTIONAL 5'-3' EXO/ENDORIBONUCLEASE RNASE J COMPND MOL_ID: 1; COMPND 2 MOLECULE: METAL DEPENDENT HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.-.-.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: O2'METHYL-RNA; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS HB27; SOURCE 3 ORGANISM_TAXID: 262724; SOURCE 4 STRAIN: HB27; SOURCE 5 GENE: TTC0775, TT_C0775; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: 16-NT 2'-O-METHYLATED RNA KEYWDS PROTEIN-RNA COMPLEX, METALLO-BETA-LACTAMASE, RNASE J, KEYWDS 2 ENDORIBONUCLEASE, 5'-3' EXORIBONUCLEASE, METAL DEPENDENT HYDROLASE, KEYWDS 3 RNA, HYDROLASE, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.DORLEANS,I.LI DE LA SIERRA-GALLAY,J.PITON,L.ZIG,L.GILET,H.PUTZER, AUTHOR 2 C.CONDON REVDAT 3 13-SEP-23 3T3N 1 REMARK SEQADV LINK REVDAT 2 29-AUG-12 3T3N 1 REMARK REVDAT 1 19-OCT-11 3T3N 0 JRNL AUTH A.DORLEANS,I.LI DE LA SIERRA-GALLAY,J.PITON,L.ZIG,L.GILET, JRNL AUTH 2 H.PUTZER,C.CONDON JRNL TITL MOLECULAR BASIS FOR THE RECOGNITION AND CLEAVAGE OF RNA BY JRNL TITL 2 THE BIFUNCTIONAL 5'-3' EXO/ENDORIBONUCLEASE RNASE J. JRNL REF STRUCTURE V. 19 1252 2011 JRNL REFN ISSN 0969-2126 JRNL PMID 21893286 JRNL DOI 10.1016/J.STR.2011.06.018 REMARK 2 REMARK 2 RESOLUTION. 3.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.8.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12301 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1004 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 3.09 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.38 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2843 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2519 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2611 REMARK 3 BIN R VALUE (WORKING SET) : 0.2483 REMARK 3 BIN FREE R VALUE : 0.2922 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.16 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 232 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4311 REMARK 3 NUCLEIC ACID ATOMS : 130 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 72.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.14890 REMARK 3 B22 (A**2) : -1.46730 REMARK 3 B33 (A**2) : -10.68160 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) : 0.585 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.873 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4550 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 6184 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1612 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 111 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 653 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4550 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 590 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4849 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.09 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 1.47 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.19 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3T3N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000066995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 REMARK 200 MONOCHROMATOR : CUT CRYOGENICALLY COOLED REMARK 200 MONOCHROMATOR CRYSTAL REMARK 200 OPTICS : KIRKPATRICK-BAEZ PAIR OF BI REMARK 200 -MORPH MIRRORS PLUS CHANNEL CUT REMARK 200 CRYOGENICALLY COOLED REMARK 200 MONOCHROMATOR CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS PACKAGE REMARK 200 DATA SCALING SOFTWARE : XDS PACKAGE, XDSCONV REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 3.090 REMARK 200 RESOLUTION RANGE LOW (A) : 55.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.64100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.930 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3BK1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-4% PEG 4K, 0.02M AMMONIUM SULFATE, REMARK 280 0.1M NA-MES, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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 58.39000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 115.64000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.39000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 115.64000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.39000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 115.64000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.39000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 115.64000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 50.97500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 115.64000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 50.97500 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 115.64000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 50.97500 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 115.64000 REMARK 290 SMTRY1 12 1.000000 0.000000 0.000000 50.97500 REMARK 290 SMTRY2 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 115.64000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 50.97500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 58.39000 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 50.97500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 58.39000 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 50.97500 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 58.39000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 50.97500 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 58.39000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 -7 REMARK 465 SER A -6 REMARK 465 HIS 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 SER A 1 REMARK 465 SER A 2 REMARK 465 GLN A 3 REMARK 465 GLY A 4 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 45.83 39.39 REMARK 500 ARG A 31 -105.48 50.81 REMARK 500 ASP A 38 154.90 67.00 REMARK 500 PRO A 44 -93.03 -78.51 REMARK 500 GLU A 45 -15.93 60.13 REMARK 500 VAL A 58 36.58 -86.35 REMARK 500 ARG A 65 -5.04 -52.18 REMARK 500 ILE A 68 96.77 -61.01 REMARK 500 ILE A 91 -72.74 -73.80 REMARK 500 PHE A 117 35.58 -86.50 REMARK 500 PRO A 131 -9.32 -57.39 REMARK 500 PRO A 163 8.60 -68.75 REMARK 500 LEU A 175 74.30 -100.60 REMARK 500 ASP A 204 107.76 -56.15 REMARK 500 ALA A 231 132.27 -31.18 REMARK 500 HIS A 243 76.15 -69.40 REMARK 500 ASP A 285 -146.11 -110.70 REMARK 500 GLU A 322 107.68 -31.44 REMARK 500 SER A 338 47.29 -77.62 REMARK 500 THR A 390 75.63 40.68 REMARK 500 ARG A 416 72.19 -113.74 REMARK 500 ASP A 545 72.89 -113.52 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 600 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 79 OD2 REMARK 620 2 ASP A 172 OD2 161.6 REMARK 620 3 HIS A 398 NE2 85.3 76.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BK1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF RNASE J REMARK 900 RELATED ID: 3BK2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF RNASE J REMARK 900 RELATED ID: 3T3O RELATED DB: PDB DBREF 3T3N A 2 554 UNP Q72JJ7 Q72JJ7_THET2 20 572 DBREF 3T3N B 901 906 PDB 3T3N 3T3N 901 906 SEQADV 3T3N MET A -7 UNP Q72JJ7 EXPRESSION TAG SEQADV 3T3N SER A -6 UNP Q72JJ7 EXPRESSION TAG SEQADV 3T3N HIS A -5 UNP Q72JJ7 EXPRESSION TAG SEQADV 3T3N HIS A -4 UNP Q72JJ7 EXPRESSION TAG SEQADV 3T3N HIS A -3 UNP Q72JJ7 EXPRESSION TAG SEQADV 3T3N HIS A -2 UNP Q72JJ7 EXPRESSION TAG SEQADV 3T3N HIS A -1 UNP Q72JJ7 EXPRESSION TAG SEQADV 3T3N HIS A 0 UNP Q72JJ7 EXPRESSION TAG SEQADV 3T3N SER A 1 UNP Q72JJ7 EXPRESSION TAG SEQADV 3T3N ALA A 77 UNP Q72JJ7 HIS 95 ENGINEERED MUTATION SEQRES 1 A 562 MET SER HIS HIS HIS HIS HIS HIS SER SER GLN GLY GLY SEQRES 2 A 562 PRO GLN ASP HIS VAL GLU ILE ILE PRO LEU GLY GLY MET SEQRES 3 A 562 GLY GLU ILE GLY LYS ASN ILE THR VAL PHE ARG PHE ARG SEQRES 4 A 562 ASP GLU ILE PHE VAL LEU ASP GLY GLY LEU ALA PHE PRO SEQRES 5 A 562 GLU GLU GLY MET PRO GLY VAL ASP LEU LEU ILE PRO ARG SEQRES 6 A 562 VAL ASP TYR LEU ILE GLU HIS ARG HIS LYS ILE LYS ALA SEQRES 7 A 562 TRP VAL LEU THR HIS GLY ALA GLU ASP HIS ILE GLY GLY SEQRES 8 A 562 LEU PRO PHE LEU LEU PRO MET ILE PHE GLY LYS GLU SER SEQRES 9 A 562 PRO VAL PRO ILE TYR GLY ALA ARG LEU THR LEU GLY LEU SEQRES 10 A 562 LEU ARG GLY LYS LEU GLU GLU PHE GLY LEU ARG PRO GLY SEQRES 11 A 562 ALA PHE ASN LEU LYS GLU ILE SER PRO ASP ASP ARG ILE SEQRES 12 A 562 GLN VAL GLY ARG TYR PHE THR LEU ASP LEU PHE ARG MET SEQRES 13 A 562 THR HIS SER ILE PRO ASP ASN SER GLY VAL VAL ILE ARG SEQRES 14 A 562 THR PRO ILE GLY THR ILE VAL HIS THR GLY ASP PHE LYS SEQRES 15 A 562 LEU ASP PRO THR PRO ILE ASP GLY LYS VAL SER HIS LEU SEQRES 16 A 562 ALA LYS VAL ALA GLN ALA GLY ALA GLU GLY VAL LEU LEU SEQRES 17 A 562 LEU ILE ALA ASP ALA THR ASN ALA GLU ARG PRO GLY TYR SEQRES 18 A 562 THR PRO SER GLU MET GLU ILE ALA LYS GLU LEU ASP ARG SEQRES 19 A 562 VAL ILE GLY ARG ALA PRO GLY ARG VAL PHE VAL THR THR SEQRES 20 A 562 PHE ALA SER HIS ILE HIS ARG ILE GLN SER VAL ILE TRP SEQRES 21 A 562 ALA ALA GLU LYS TYR GLY ARG LYS VAL ALA MET GLU GLY SEQRES 22 A 562 ARG SER MET LEU LYS PHE SER ARG ILE ALA LEU GLU LEU SEQRES 23 A 562 GLY TYR LEU LYS VAL LYS ASP ARG LEU TYR THR LEU GLU SEQRES 24 A 562 GLU VAL LYS ASP LEU PRO ASP HIS GLN VAL LEU ILE LEU SEQRES 25 A 562 ALA THR GLY SER GLN GLY GLN PRO MET SER VAL LEU HIS SEQRES 26 A 562 ARG LEU ALA PHE GLU GLY HIS ALA LYS MET ALA ILE LYS SEQRES 27 A 562 PRO GLY ASP THR VAL ILE LEU SER SER SER PRO ILE PRO SEQRES 28 A 562 GLY ASN GLU GLU ALA VAL ASN ARG VAL ILE ASN ARG LEU SEQRES 29 A 562 TYR ALA LEU GLY ALA TYR VAL LEU TYR PRO PRO THR TYR SEQRES 30 A 562 LYS VAL HIS ALA SER GLY HIS ALA SER GLN GLU GLU LEU SEQRES 31 A 562 LYS LEU ILE LEU ASN LEU THR THR PRO ARG PHE PHE LEU SEQRES 32 A 562 PRO TRP HIS GLY GLU VAL ARG HIS GLN MET ASN PHE LYS SEQRES 33 A 562 TRP LEU ALA GLU SER MET SER ARG PRO PRO GLU LYS THR SEQRES 34 A 562 LEU ILE GLY GLU ASN GLY ALA VAL TYR ARG LEU THR ARG SEQRES 35 A 562 GLU THR PHE GLU LYS VAL GLY GLU VAL PRO HIS GLY VAL SEQRES 36 A 562 LEU TYR VAL ASP GLY LEU GLY VAL GLY ASP ILE THR GLU SEQRES 37 A 562 GLU ILE LEU ALA ASP ARG ARG HIS MET ALA GLU GLU GLY SEQRES 38 A 562 LEU VAL VAL ILE THR ALA LEU ALA GLY GLU ASP PRO VAL SEQRES 39 A 562 VAL GLU VAL VAL SER ARG GLY PHE VAL LYS ALA GLY GLU SEQRES 40 A 562 ARG LEU LEU GLY GLU VAL ARG ARG MET ALA LEU GLU ALA SEQRES 41 A 562 LEU LYS ASN GLY VAL ARG GLU LYS LYS PRO LEU GLU ARG SEQRES 42 A 562 ILE ARG ASP ASP ILE TYR TYR PRO VAL LYS LYS PHE LEU SEQRES 43 A 562 LYS LYS ALA THR GLY ARG ASP PRO MET ILE LEU PRO VAL SEQRES 44 A 562 VAL ILE GLU SEQRES 1 B 6 OMU OMU OMC OMC OMG OMU MODRES 3T3N OMU B 901 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 3T3N OMU B 902 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 3T3N OMC B 903 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 3T3N OMC B 904 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 3T3N OMG B 905 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 3T3N OMU B 906 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE HET OMU B 901 22 HET OMU B 902 21 HET OMC B 903 21 HET OMC B 904 21 HET OMG B 905 24 HET OMU B 906 21 HET ZN A 600 1 HETNAM OMU O2'-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 2 OMU 3(C10 H15 N2 O9 P) FORMUL 2 OMC 2(C10 H16 N3 O8 P) FORMUL 2 OMG C11 H16 N5 O8 P FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *13(H2 O) HELIX 1 1 VAL A 58 HIS A 64 1 7 HELIX 2 2 ALA A 77 GLY A 82 1 6 HELIX 3 3 GLY A 83 PHE A 92 1 10 HELIX 4 4 ALA A 103 PHE A 117 1 15 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 THR A 289 LYS A 294 1 6 HELIX 10 10 PRO A 297 HIS A 299 5 3 HELIX 11 11 SER A 314 PHE A 321 1 8 HELIX 12 12 ASN A 345 GLY A 360 1 16 HELIX 13 13 SER A 378 THR A 390 1 13 HELIX 14 14 VAL A 401 SER A 413 1 13 HELIX 15 15 THR A 459 GLY A 473 1 15 HELIX 16 16 VAL A 495 LEU A 501 1 7 HELIX 17 17 LEU A 501 GLU A 519 1 19 HELIX 18 18 PRO A 522 THR A 542 1 21 SHEET 1 A 8 PHE A 124 GLU A 128 0 SHEET 2 A 8 SER A 96 GLY A 102 1 N ILE A 100 O ASN A 125 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 GLY A 441 N VAL A 429 SHEET 1 B 2 MET A 18 GLY A 19 0 SHEET 2 B 2 GLY A 399 GLU A 400 1 O GLY A 399 N GLY A 19 SHEET 1 C 2 LEU A 53 PRO A 56 0 SHEET 2 C 2 VAL A 447 VAL A 450 -1 O LEU A 448 N ILE A 55 SHEET 1 D 7 ARG A 134 VAL A 137 0 SHEET 2 D 7 PHE A 141 ARG A 147 -1 O LEU A 143 N ILE A 135 SHEET 3 D 7 SER A 156 THR A 162 -1 O VAL A 159 N ASP A 144 SHEET 4 D 7 GLY A 165 GLY A 171 -1 O HIS A 169 N VAL A 158 SHEET 5 D 7 VAL A 198 ASP A 204 1 O ILE A 202 N VAL A 168 SHEET 6 D 7 PRO A 391 TRP A 397 1 O PHE A 393 N LEU A 199 SHEET 7 D 7 LYS A 420 THR A 421 1 O LYS A 420 N PHE A 394 SHEET 1 E 5 LYS A 260 MET A 263 0 SHEET 2 E 5 VAL A 301 ALA A 305 1 O LEU A 302 N ALA A 262 SHEET 3 E 5 VAL A 235 THR A 238 1 N VAL A 237 O ALA A 305 SHEET 4 E 5 THR A 334 LEU A 337 1 O ILE A 336 N PHE A 236 SHEET 5 E 5 TYR A 362 LEU A 364 1 O LEU A 364 N VAL A 335 SHEET 1 F 3 VAL A 487 ARG A 492 0 SHEET 2 F 3 LEU A 474 LEU A 480 -1 N VAL A 476 O VAL A 490 SHEET 3 F 3 MET A 547 ILE A 553 1 O MET A 547 N VAL A 475 LINK O3' OMU B 901 P OMU B 902 1555 1555 1.60 LINK O3' OMU B 902 P OMC B 903 1555 1555 1.61 LINK O3' OMC B 903 P OMC B 904 1555 1555 1.60 LINK O3' OMC B 904 P OMG B 905 1555 1555 1.61 LINK O3' OMG B 905 P OMU B 906 1555 1555 1.61 LINK OD2 ASP A 79 ZN ZN A 600 1555 1555 1.96 LINK OD2 ASP A 172 ZN ZN A 600 1555 1555 1.89 LINK NE2 HIS A 398 ZN ZN A 600 1555 1555 2.56 CISPEP 1 GLU A 322 GLY A 323 0 0.63 CISPEP 2 PRO A 366 PRO A 367 0 6.66 SITE 1 AC1 5 HIS A 75 ASP A 79 HIS A 80 ASP A 172 SITE 2 AC1 5 HIS A 398 CRYST1 101.950 116.780 231.280 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 0.009809 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004324 0.00000