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 7 30-AUG-23 2FK6 1 REMARK 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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