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- PDB-2jan: TYROSYL-TRNA SYNTHETASE FROM MYCOBACTERIUM TUBERCULOSIS IN UNLIGA... -

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Basic information

Entry
Database: PDB / ID: 2jan
TitleTYROSYL-TRNA SYNTHETASE FROM MYCOBACTERIUM TUBERCULOSIS IN UNLIGANDED STATE
ComponentsTYROSYL-TRNA SYNTHETASE
KeywordsLIGASE / PROTEIN BIOSYNTHESIS / AMINOACYL-TRNA SYNTHETASE / TRNA / TYRRS / TYROSINE / RNA-BINDING / ATP-BINDING / AMINOACYLATION / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / cell wall / RNA binding / ATP binding / plasma membrane / cytosol
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site ...Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 RNA-binding domain profile. / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHartmann, M.D. / Shkolnaya, L.A. / Bourenkov, G.P. / Strizhov, N.I. / Bartunik, H.D.
CitationJournal: To be Published
Title: The Structure of Tyrosyl-tRNA Synthetase from Mycobacterium Tuberculosis
Authors: Hartmann, M.D. / Shkolnaya, L.A. / Bourenkov, G.P. / Strizhov, N.I. / Bartunik, H.D.
History
DepositionNov 29, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYROSYL-TRNA SYNTHETASE
B: TYROSYL-TRNA SYNTHETASE
C: TYROSYL-TRNA SYNTHETASE
D: TYROSYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)189,8304
Polymers189,8304
Non-polymers00
Water1,892105
1
A: TYROSYL-TRNA SYNTHETASE
D: TYROSYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)94,9152
Polymers94,9152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-36.7 kcal/mol
Surface area44320 Å2
MethodPQS
2
B: TYROSYL-TRNA SYNTHETASE
C: TYROSYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)94,9152
Polymers94,9152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-39.7 kcal/mol
Surface area44150 Å2
MethodPQS
Unit cell
Length a, b, c (Å)71.262, 78.440, 81.633
Angle α, β, γ (deg.)74.42, 83.19, 82.95
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13B
23C
33D
14A
24B
15C
25D
16C
26D
17A
27B
18A
28B
19A
29B
110C
210D
111C
211D
112C
212D
113C
213D
114A
214B
115A
215B
116A
216B
117A
217B
118A
218B
318C
418D
119A
219B
120C
220D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A5 - 38
2111B5 - 38
1121C5 - 39
2121D5 - 39
1131B40 - 46
2131C40 - 46
3131D40 - 46
1141A47 - 77
2141B47 - 77
1151C47 - 61
2151D47 - 61
1161C63 - 77
2161D63 - 77
1171A105 - 113
2171B105 - 113
1181A114 - 125
2181B114 - 125
1191A127 - 161
2191B127 - 161
11101C102 - 111
21101D102 - 111
11111C112 - 116
21111D112 - 116
11121C117 - 141
21121D117 - 141
11131C143 - 205
21131D143 - 205
11141A163 - 326
21141B163 - 326
11151A328 - 370
21151B328 - 370
11161A372 - 378
21161B372 - 378
11171A383 - 396
21171B383 - 396
11181A397 - 400
21181B397 - 400
31181C397 - 400
41181D397 - 400
11191A401 - 424
21191B401 - 424
11201C207 - 424
21201D207 - 424

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20

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Components

#1: Protein
TYROSYL-TRNA SYNTHETASE / TYROSINE-TRNA LIGASE / TYRRS


Mass: 47457.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HIS-TAG (LEHHHHHH) / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P67611, UniProt: P9WFT1*PLUS, tyrosine-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL HIS-TAG (LEHHHHHH)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 10% (W/V) PEG 6000, 1 M LICL, 0.1 M HEPES AT PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 2, 2005 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.9→19.89 Å / Num. obs: 36581 / % possible obs: 98.4 % / Redundancy: 2.92 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.63
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.86 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TS1

2ts1


Resolution: 2.9→19.89 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.879 / SU B: 18.497 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1864 5.1 %RANDOM
Rwork0.201 ---
obs0.204 34713 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0.44 Å2-0.16 Å2
2---1.27 Å22.53 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12468 0 0 105 12573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02112736
X-RAY DIFFRACTIONr_bond_other_d0.0060.028495
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.94617317
X-RAY DIFFRACTIONr_angle_other_deg0.946320508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50751635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8922.619569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.766151995
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.69915127
X-RAY DIFFRACTIONr_chiral_restr0.060.21970
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022752
X-RAY DIFFRACTIONr_nbd_refined0.2170.23062
X-RAY DIFFRACTIONr_nbd_other0.1920.28730
X-RAY DIFFRACTIONr_nbtor_refined0.1770.26285
X-RAY DIFFRACTIONr_nbtor_other0.0820.27165
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2308
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.14838353
X-RAY DIFFRACTIONr_mcbond_other0.09133376
X-RAY DIFFRACTIONr_mcangle_it1.752412861
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28165069
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.81294454
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A422tight positional0.020.05
21C442tight positional0.020.05
31B80tight positional0.020.05
32C80tight positional0.020.05
33D80tight positional0.020.05
41A402tight positional0.020.05
51C215tight positional0.020.05
61C163tight positional0.020.05
71A141tight positional0.030.05
81A139tight positional0.020.05
91A476tight positional0.020.05
101C153tight positional0.020.05
111C63tight positional0.010.05
121C316tight positional0.020.05
131C858tight positional0.020.05
141A2117tight positional0.030.05
151A428tight positional0.010.05
161A58tight positional0.010.05
171A172tight positional0.010.05
181A41tight positional0.010.05
182B41tight positional0.020.05
183C41tight positional0.010.05
184D41tight positional0.010.05
191A302tight positional0.020.05
201C2715tight positional0.020.05
11A422tight thermal0.090.5
21C442tight thermal0.050.5
31B80tight thermal0.050.5
32C80tight thermal0.030.5
33D80tight thermal0.050.5
41A402tight thermal0.060.5
51C215tight thermal0.050.5
61C163tight thermal0.050.5
71A141tight thermal0.050.5
81A139tight thermal0.050.5
91A476tight thermal0.050.5
101C153tight thermal0.050.5
111C63tight thermal0.040.5
121C316tight thermal0.060.5
131C858tight thermal0.10.5
141A2117tight thermal0.070.5
151A428tight thermal0.030.5
161A58tight thermal0.030.5
171A172tight thermal0.060.5
181A41tight thermal0.050.5
182B41tight thermal0.050.5
183C41tight thermal0.040.5
184D41tight thermal0.050.5
191A302tight thermal0.110.5
201C2715tight thermal0.050.5
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 142 -
Rwork0.318 2469 -
obs--97.61 %

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