HEADER HYDROLASE/RNA 04-JAN-06 2FK6 TITLE CRYSTAL STRUCTURE OF RNASE Z/TRNA(THR) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA(THR); COMPND 3 CHAIN: R; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RIBONUCLEASE Z; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: RNASE Z; TRNASE Z; TRNA 3 ENDONUCLEASE; COMPND 9 EC: 3.1.26.11; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: B.SUBTILIS TRNATHR(ENCODED BY THE TRN1-THR GENE) WAS SOURCE 4 TRANSCRIBED IN VITRO AS A PRECURSOR WITH 6 NT 3'-EXTENSION FROM PCR SOURCE 5 FRAGMENT GENERATED FROM PLASMID PHMT1, USING OLIGONUCLEOTIDES HP560 SOURCE 6 AND CC079; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 9 ORGANISM_TAXID: 1423; SOURCE 10 STRAIN: W168; SOURCE 11 GENE: RNZ; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS (LAMBDADE3)-RIL; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS PROTEIN-TRNA COMPLEX; ZINC-DEPENDENT METAL HYDROLASE; TRNA MATURASE, KEYWDS 2 HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR I.LI DE LA SIERRA-GALLAY,N.MATHY,O.PELLEGRINI,C.CONDON REVDAT 6 20-OCT-21 2FK6 1 REMARK SEQADV LINK REVDAT 5 18-OCT-17 2FK6 1 REMARK REVDAT 4 13-JUL-11 2FK6 1 VERSN REVDAT 3 24-FEB-09 2FK6 1 VERSN REVDAT 2 06-JUN-06 2FK6 1 JRNL REVDAT 1 21-MAR-06 2FK6 0 JRNL AUTH I.LI DE LA SIERRA-GALLAY,N.MATHY,O.PELLEGRINI,C.CONDON JRNL TITL STRUCTURE OF THE UBIQUITOUS 3' PROCESSING ENZYME RNASE Z JRNL TITL 2 BOUND TO TRANSFER RNA. JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 376 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 16518398 JRNL DOI 10.1038/NSMB1066 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.LI DE LA SIERRA-GALLAY,O.PELLEGRINI,C.CONDON REMARK 1 TITL STRUCTURAL BASIS FOR SUBSTRATE BINDING, CLEAVAGE AND REMARK 1 TITL 2 ALLOSTERY IN THE TRNA MATURASE RNASE Z REMARK 1 REF NATURE V. 433 657 2005 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 2.90 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 882652.530 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 15022 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) : 0.250 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 747 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2160 REMARK 3 BIN R VALUE (WORKING SET) : 0.3460 REMARK 3 BIN FREE R VALUE : 0.3620 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 114 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.034 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2395 REMARK 3 NUCLEIC ACID ATOMS : 1125 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 11 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 250.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -19.63000 REMARK 3 B22 (A**2) : 0.44000 REMARK 3 B33 (A**2) : 19.19000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 13.54000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.46 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) : 0.50 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.58 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.980 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.230 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.150 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.420 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.270 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 64.48 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : LIGAND_XPLOR_PAR.TXT REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : &_1_TOPOLOGY_INFILE_1 REMARK 3 TOPOLOGY FILE 2 : &_1_TOPOLOGY_INFILE_2 REMARK 3 TOPOLOGY FILE 3 : &_1_TOPOLOGY_INFILE_3 REMARK 3 TOPOLOGY FILE 4 : &_1_TOPOLOGY_INFILE_4 REMARK 3 TOPOLOGY FILE 5 : &_1_TOPOLOGY_INFILE_5 REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FK6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000035974. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : 2 SILICON CRYSTALS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15022 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 47.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.49600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1Y44 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG MME 2000, 0.1M NA-MES, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 86.77000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 86.77000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.20000 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY REMARK 300 THE TWO FOLD AXIS: -X,Y,-Z 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: R, 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 289.51201 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 94.23753 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 A R 26 REMARK 465 C R 27 REMARK 465 U R 28 REMARK 465 U R 29 REMARK 465 C R 30 REMARK 465 C R 31 REMARK 465 A R 32 REMARK 465 U R 33 REMARK 465 G R 34 REMARK 465 G R 35 REMARK 465 U R 36 REMARK 465 A R 37 REMARK 465 A R 38 REMARK 465 G R 39 REMARK 465 G R 40 REMARK 465 A R 41 REMARK 465 A R 42 REMARK 465 G R 43 REMARK 465 A R 44 REMARK 465 G R 45 REMARK 465 U R 74 REMARK 465 A R 75 REMARK 465 A R 76 REMARK 465 A R 77 REMARK 465 U R 78 REMARK 465 G R 79 REMARK 465 LYS A 308 REMARK 465 LEU A 309 REMARK 465 ALA A 310 REMARK 465 ALA A 311 REMARK 465 ALA A 312 REMARK 465 LEU A 313 REMARK 465 GLU A 314 REMARK 465 HIS A 315 REMARK 465 HIS A 316 REMARK 465 HIS A 317 REMARK 465 HIS A 318 REMARK 465 HIS A 319 REMARK 465 HIS A 320 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 R 46 P OP1 OP2 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 U R 66 C2' - C3' - O3' ANGL. DEV. = 11.3 DEGREES REMARK 500 G R 67 C4' - C3' - O3' ANGL. DEV. = 12.4 DEGREES REMARK 500 G R 67 C2' - C3' - O3' ANGL. DEV. = 9.7 DEGREES REMARK 500 G R 68 C4' - C3' - O3' ANGL. DEV. = 12.3 DEGREES REMARK 500 A R 69 C2' - C3' - O3' ANGL. DEV. = 9.9 DEGREES REMARK 500 G R 71 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 C R 72 C4' - C3' - O3' ANGL. DEV. = 14.0 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 THR A 20 142.77 -30.99 REMARK 500 SER A 21 109.80 164.65 REMARK 500 ARG A 30 20.08 -153.82 REMARK 500 ASP A 37 145.50 68.42 REMARK 500 LEU A 47 -3.62 -58.57 REMARK 500 ARG A 54 -19.60 -47.71 REMARK 500 HIS A 63 139.21 -170.63 REMARK 500 ALA A 65 113.96 -168.15 REMARK 500 THR A 112 27.25 -77.10 REMARK 500 GLU A 122 138.83 -28.02 REMARK 500 ASP A 128 -152.81 -152.42 REMARK 500 HIS A 140 17.29 -163.27 REMARK 500 GLU A 143 45.88 75.73 REMARK 500 VAL A 173 -12.78 -44.59 REMARK 500 ASP A 187 41.95 -98.49 REMARK 500 PHE A 196 44.50 -106.27 REMARK 500 ASP A 224 -0.11 57.68 REMARK 500 CYS A 225 159.33 -45.42 REMARK 500 ASP A 238 36.96 -69.73 REMARK 500 HIS A 247 -164.73 -108.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 G R 71 0.07 SIDE CHAIN 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 67 OD2 REMARK 620 2 HIS A 68 NE2 90.3 REMARK 620 3 ASP A 211 OD2 167.8 101.2 REMARK 620 4 HIS A 269 NE2 84.5 99.6 89.4 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 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y44 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TRNASE Z FROM BACILLUS SUBTILIS REMARK 900 RELATED ID: 1WW1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TRNASE Z FROM THERMOTOGA MARITIMA DBREF 2FK6 A 1 307 UNP P54548 RNZ_BACSU 1 307 DBREF1 2FK6 R 1 79 GB Z99104 DBREF2 2FK6 R 32468687 165829 165907 SEQADV 2FK6 MET A 46 UNP P54548 ILE 46 ENGINEERED MUTATION SEQADV 2FK6 ALA A 65 UNP P54548 HIS 65 ENGINEERED MUTATION SEQADV 2FK6 MET A 228 UNP P54548 LEU 228 ENGINEERED MUTATION SEQADV 2FK6 LYS A 308 UNP P54548 EXPRESSION TAG SEQADV 2FK6 LEU A 309 UNP P54548 EXPRESSION TAG SEQADV 2FK6 ALA A 310 UNP P54548 EXPRESSION TAG SEQADV 2FK6 ALA A 311 UNP P54548 EXPRESSION TAG SEQADV 2FK6 ALA A 312 UNP P54548 EXPRESSION TAG SEQADV 2FK6 LEU A 313 UNP P54548 EXPRESSION TAG SEQADV 2FK6 GLU A 314 UNP P54548 EXPRESSION TAG SEQADV 2FK6 HIS A 315 UNP P54548 EXPRESSION TAG SEQADV 2FK6 HIS A 316 UNP P54548 EXPRESSION TAG SEQADV 2FK6 HIS A 317 UNP P54548 EXPRESSION TAG SEQADV 2FK6 HIS A 318 UNP P54548 EXPRESSION TAG SEQADV 2FK6 HIS A 319 UNP P54548 EXPRESSION TAG SEQADV 2FK6 HIS A 320 UNP P54548 EXPRESSION TAG SEQRES 1 R 79 G C U U C C A U A G C U C SEQRES 2 R 79 A G C A G G U A G A G C A SEQRES 3 R 79 C U U C C A U G G U A A G SEQRES 4 R 79 G A A G A G G U C A G C G SEQRES 5 R 79 G U U C G A G C C C G C U SEQRES 6 R 79 U G G A A G C U U A A A U SEQRES 7 R 79 G SEQRES 1 A 320 MET GLU LEU LEU PHE LEU GLY THR GLY ALA GLY ILE PRO SEQRES 2 A 320 ALA LYS ALA ARG ASN VAL THR SER VAL ALA LEU LYS LEU SEQRES 3 A 320 LEU GLU GLU ARG ARG SER VAL TRP LEU PHE ASP CYS GLY SEQRES 4 A 320 GLU ALA THR GLN HIS GLN MET LEU HIS THR THR ILE LYS SEQRES 5 A 320 PRO ARG LYS ILE GLU LYS ILE PHE ILE THR HIS MET ALA SEQRES 6 A 320 GLY ASP HIS VAL TYR GLY LEU PRO GLY LEU LEU GLY SER SEQRES 7 A 320 ARG SER PHE GLN GLY GLY GLU ASP GLU LEU THR VAL TYR SEQRES 8 A 320 GLY PRO LYS GLY ILE LYS ALA PHE ILE GLU THR SER LEU SEQRES 9 A 320 ALA VAL THR LYS THR HIS LEU THR TYR PRO LEU ALA ILE SEQRES 10 A 320 GLN GLU ILE GLU GLU GLY ILE VAL PHE GLU ASP ASP GLN SEQRES 11 A 320 PHE ILE VAL THR ALA VAL SER VAL ILE HIS GLY VAL GLU SEQRES 12 A 320 ALA PHE GLY TYR ARG VAL GLN GLU LYS ASP VAL PRO GLY SEQRES 13 A 320 SER LEU LYS ALA ASP VAL LEU LYS GLU MET ASN ILE PRO SEQRES 14 A 320 PRO GLY PRO VAL TYR GLN LYS ILE LYS LYS GLY GLU THR SEQRES 15 A 320 VAL THR LEU GLU ASP GLY ARG ILE ILE ASN GLY ASN ASP SEQRES 16 A 320 PHE LEU GLU PRO PRO LYS LYS GLY ARG SER VAL VAL PHE SEQRES 17 A 320 SER GLY ASP THR ARG VAL SER ASP LYS LEU LYS GLU LEU SEQRES 18 A 320 ALA ARG ASP CYS ASP VAL MET VAL HIS GLU ALA THR PHE SEQRES 19 A 320 ALA LYS GLU ASP ARG LYS LEU ALA TYR ASP TYR TYR HIS SEQRES 20 A 320 SER THR THR GLU GLN ALA ALA VAL THR ALA LYS GLU ALA SEQRES 21 A 320 ARG ALA LYS GLN LEU ILE LEU THR HIS ILE SER ALA ARG SEQRES 22 A 320 TYR GLN GLY ASP ALA SER LEU GLU LEU GLN LYS GLU ALA SEQRES 23 A 320 VAL ASP VAL PHE PRO ASN SER VAL ALA ALA TYR ASP PHE SEQRES 24 A 320 LEU GLU VAL ASN VAL PRO ARG GLY LYS LEU ALA ALA ALA SEQRES 25 A 320 LEU GLU HIS HIS HIS HIS HIS HIS HET ZN A 401 1 HET MES A 801 12 HET GOL A 501 6 HETNAM ZN ZINC ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN ZN 2+ FORMUL 4 MES C6 H13 N O4 S FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *11(H2 O) HELIX 1 1 LEU A 27 ARG A 31 1 5 HELIX 2 2 ALA A 41 LEU A 47 1 7 HELIX 3 3 LYS A 52 ARG A 54 5 3 HELIX 4 4 ALA A 65 TYR A 70 1 6 HELIX 5 5 GLY A 71 GLN A 82 1 12 HELIX 6 6 GLY A 95 THR A 107 1 13 HELIX 7 7 LYS A 159 LYS A 164 1 6 HELIX 8 8 PRO A 172 LYS A 179 1 8 HELIX 9 9 ASN A 194 LEU A 197 5 4 HELIX 10 10 SER A 215 ALA A 222 1 8 HELIX 11 11 ASP A 238 TYR A 246 1 9 HELIX 12 12 THR A 249 ARG A 261 1 13 HELIX 13 13 ASP A 277 ASP A 288 1 12 SHEET 1 A 7 LEU A 115 GLU A 119 0 SHEET 2 A 7 LEU A 88 GLY A 92 1 N VAL A 90 O GLN A 118 SHEET 3 A 7 ILE A 56 PHE A 60 1 N ILE A 59 O TYR A 91 SHEET 4 A 7 SER A 32 PHE A 36 1 N LEU A 35 O PHE A 60 SHEET 5 A 7 SER A 21 LEU A 26 -1 N LEU A 24 O TRP A 34 SHEET 6 A 7 GLU A 2 GLY A 7 -1 N GLU A 2 O LYS A 25 SHEET 7 A 7 GLU A 301 ASN A 303 -1 O VAL A 302 N LEU A 3 SHEET 1 B 7 GLY A 123 GLU A 127 0 SHEET 2 B 7 PHE A 131 SER A 137 -1 O VAL A 133 N VAL A 125 SHEET 3 B 7 PHE A 145 GLU A 151 -1 O GLN A 150 N ILE A 132 SHEET 4 B 7 SER A 205 PHE A 208 -1 O PHE A 208 N TYR A 147 SHEET 5 B 7 VAL A 227 GLU A 231 1 O VAL A 229 N VAL A 207 SHEET 6 B 7 GLN A 264 THR A 268 1 O THR A 268 N HIS A 230 SHEET 7 B 7 SER A 293 ALA A 295 1 O VAL A 294 N LEU A 267 SHEET 1 C 2 THR A 182 THR A 184 0 SHEET 2 C 2 ILE A 190 ASN A 192 -1 O ILE A 191 N VAL A 183 LINK OD2 ASP A 67 ZN ZN A 401 1555 1555 2.56 LINK NE2 HIS A 68 ZN ZN A 401 1555 1555 2.54 LINK OD2 ASP A 211 ZN ZN A 401 1555 1555 2.20 LINK NE2 HIS A 269 ZN ZN A 401 1555 1555 2.55 SITE 1 AC1 4 ASP A 67 HIS A 68 ASP A 211 HIS A 269 SITE 1 AC2 5 ARG A 31 SER A 32 ARG A 54 GLU A 57 SITE 2 AC2 5 ASP A 86 SITE 1 AC3 4 LYS A 164 GLU A 165 ARG A 223 ASP A 224 CRYST1 173.540 42.400 110.430 90.00 121.42 90.00 C 1 2 1 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 0.005762 0.000000 0.003520 0.00000 SCALE2 0.000000 0.023585 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010611 0.00000 MASTER 393 0 3 13 16 0 4 6 0 0 0 32 END