10 20 30 40 50 60 70 80 2HKZ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LIGASE 06-JUL-06 2HKZ
TITLE CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF THREONYL-TRNA TITLE 2 SYNTHETASE FROM PYROCOCCUS ABYSSI IN COMPLEX WITH L-SERINE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: THREONYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EDITING DOMAIN (RESIDUES 1-143); COMPND 5 SYNONYM: THREONINE--TRNA LIGASE, THRRS; COMPND 6 EC: 6.1.1.3; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI; SOURCE 3 ORGANISM_TAXID: 29292; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21B
KEYWDS TRANSLATION, EDITING, AMINOACYL-TRNA SYNTHETASE, ENZYME KEYWDS 2 MECHANISM, ENANTIOSELECTIVITY, LIGASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.DWIVEDI,S.P.KRUPARANI,R.SANKARANARAYANAN
REVDAT 3 24-FEB-09 2HKZ 1 VERSN REVDAT 2 19-SEP-06 2HKZ 1 JRNL REVDAT 1 29-AUG-06 2HKZ 0
JRNL AUTH T.HUSSAIN,S.P.KRUPARANI,B.PAL,A.C.DOCK-BREGEON, JRNL AUTH 2 S.DWIVEDI,M.R.SHEKAR,K.SURESHBABU, JRNL AUTH 3 R.SANKARANARAYANAN JRNL TITL POST-TRANSFER EDITING MECHANISM OF A JRNL TITL 2 D-AMINOACYL-TRNA DEACYLASE-LIKE DOMAIN IN JRNL TITL 3 THREONYL-TRNA SYNTHETASE FROM ARCHAEA JRNL REF EMBO J. V. 25 4152 2006 JRNL REFN ISSN 0261-4189 JRNL PMID 16902403 JRNL DOI 10.1038/SJ.EMBOJ.7601278
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.DWIVEDI,S.P.KRUPARANI,R.SANKARANARAYANAN REMARK 1 TITL A D-AMINO ACID EDITING MODULE COUPLED TO THE REMARK 1 TITL 2 TRANSLATIONAL APPARATUS IN ARCHAEA REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 12 556 2005 REMARK 1 REFN ISSN 1545-9993 REMARK 1 PMID 15908961 REMARK 1 DOI 10.1038/NSMB943
REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 24.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1299462.820 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 8399 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) : 0.220 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 441 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.014 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1147 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 78 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1140 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.85000 REMARK 3 B22 (A**2) : -2.85000 REMARK 3 B33 (A**2) : 5.70000 REMARK 3 B12 (A**2) : -1.09000 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.24 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) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.69 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 63.33 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : LSN_NEW.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : LSN_NEW.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2HKZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUL-06. REMARK 100 THE RCSB ID CODE IS RCSB038466.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8413 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.7700 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) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.38800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.850 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 (MOLREP) REMARK 200 STARTING MODEL: PDB ENTRY 1Y2Q REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 8000, 0.1M HEPES, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.07133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.53567 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.53567 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.07133 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 BIOLOGICAL ASSEMBLY IS A DIMER
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 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 -0.500000 -0.866025 0.000000 92.85900 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 53.61217 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 43.07133
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 LYS A 18 CG CD CE NZ
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 16 -139.33 -120.93 REMARK 500 ASN A 22 67.01 -117.86 REMARK 500 PRO A 23 -170.95 -66.59 REMARK 500 ASN A 52 79.29 -159.98 REMARK 500 GLU A 134 87.17 -155.51 REMARK 500 GLU A 142 35.26 -62.37 REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SER A 201
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y2Q RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITHOUT LIGAND REMARK 900 RELATED ID: 2HL0 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH SERYL-3'-AMINOADENOSINE REMARK 900 RELATED ID: 2HL1 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH SERYL-3'-AMINOADENOSINE REMARK 900 RELATED ID: 2HL2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH AN ANALOG OF SERYLADENYLATE
DBREF 2HKZ A 1 143 UNP Q9UZ14 SYT_PYRAB 1 143
SEQRES 1 A 143 MET ARG VAL LEU LEU ILE HIS SER ASP TYR ILE GLU TYR SEQRES 2 A 143 GLU VAL LYS ASP LYS ALA LEU LYS ASN PRO GLU PRO ILE SEQRES 3 A 143 SER GLU ASP MET LYS ARG GLY ARG MET GLU GLU VAL LEU SEQRES 4 A 143 VAL ALA PHE ILE SER VAL GLU LYS VAL ASP GLU LYS ASN SEQRES 5 A 143 PRO GLU GLU VAL SER LEU LYS ALA ILE GLU GLU ILE SER SEQRES 6 A 143 LYS VAL ALA GLU GLN VAL LYS ALA GLU ASN VAL PHE VAL SEQRES 7 A 143 TYR PRO PHE ALA HIS LEU SER SER GLU LEU ALA LYS PRO SEQRES 8 A 143 SER VAL ALA MET ASP ILE LEU ASN ARG VAL TYR GLN GLY SEQRES 9 A 143 LEU LYS GLU ARG GLY PHE ASN VAL GLY LYS ALA PRO PHE SEQRES 10 A 143 GLY TYR TYR LYS ALA PHE LYS ILE SER CYS LYS GLY HIS SEQRES 11 A 143 PRO LEU ALA GLU LEU SER ARG THR ILE VAL PRO GLU GLU
HET SER A 201 7
HETNAM SER SERINE
FORMUL 2 SER C3 H7 N O3 FORMUL 3 HOH *106(H2 O)
HELIX 1 1 SER A 27 MET A 30 5 4 HELIX 2 2 GLU A 46 LYS A 51 5 6 HELIX 3 3 ASN A 52 VAL A 71 1 20 HELIX 4 4 LYS A 90 ARG A 108 1 19
SHEET 1 A 5 ASN A 111 LYS A 114 0 SHEET 2 A 5 ASN A 75 PRO A 80 1 N VAL A 76 O GLY A 113 SHEET 3 A 5 ARG A 32 SER A 44 1 N ALA A 41 O PHE A 77 SHEET 4 A 5 ARG A 2 LYS A 18 -1 N SER A 8 O VAL A 38 SHEET 5 A 5 TYR A 119 CYS A 127 -1 O TYR A 120 N ASP A 17 SHEET 1 B 5 ASN A 111 LYS A 114 0 SHEET 2 B 5 ASN A 75 PRO A 80 1 N VAL A 76 O GLY A 113 SHEET 3 B 5 ARG A 32 SER A 44 1 N ALA A 41 O PHE A 77 SHEET 4 B 5 ARG A 2 LYS A 18 -1 N SER A 8 O VAL A 38 SHEET 5 B 5 GLU A 134 THR A 138 -1 O LEU A 135 N LEU A 5
SITE 1 AC1 5 PRO A 80 PHE A 117 GLY A 118 LYS A 121 SITE 2 AC1 5 HOH A 247
CRYST1 61.906 61.906 64.607 90.00 90.00 120.00 P 32 2 1 6
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 0.016154 0.009326 0.000000 0.00000
SCALE2 0.000000 0.018652 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015478 0.00000