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- PDB-1h4v: HISTIDYL-TRNA SYNTHETASE from Thermus Thermophilus (ligand free) -

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Basic information

Entry
Database: PDB / ID: 1h4v
TitleHISTIDYL-TRNA SYNTHETASE from Thermus Thermophilus (ligand free)
ComponentsHISTIDYL-TRNA SYNTHETASE
KeywordsTRNA SYNTHETASE / CLASS IIA AMINOACYL-TRNA SYNTHETASE / ATP + L-HISTIDINE TRNA(HIS)-> AMP + PPI + L-HISTIDYL-TRNA(HIS)
Function / homology
Function and homology information


histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histidine--tRNA ligase / Histidine--tRNA ligase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCusack, S. / Yaremchuk, A. / Tukalo, M.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: A Succession of Substrate Induced Conformational Changes Ensures the Amino Acid Specificity of Thermus Thermophilus Prolyl-tRNA Synthetase: Comparison with Histidyl-tRNA Synthetase
Authors: Yaremchuk, A. / Tukalo, M. / Grotli, M. / Cusack, S.
#1: Journal: Biochemistry / Year: 1997
Title: Crystal Structure Analysis of the Activation of Histidine by Thermus Thermophilus Histidyl-tRNA Synthetase
Authors: Aberg, A. / Yaremchuk, A. / Tukalo, M. / Rasmussen, B. / Cusack, S.
History
DepositionMay 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2001Provider: 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

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Assembly

Deposited unit
B: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2222
Polymers47,1261
Non-polymers961
Water1,17165
1
B: HISTIDYL-TRNA SYNTHETASE
hetero molecules

B: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4444
Polymers94,2522
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)111.130, 102.150, 91.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HISTIDYL-TRNA SYNTHETASE


Mass: 47125.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: LIGAND FREE FORM OF THE ENZYME / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB27
References: UniProt: P56194, UniProt: P62374*PLUS, histidine-tRNA ligase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF T. THERMOPHILUS HISTIDYL-TRNA SYNTHETASE IS GIVEN IN BIOCHEMISTRY 36, 3084 - 3094, ...THE SEQUENCE OF T. THERMOPHILUS HISTIDYL-TRNA SYNTHETASE IS GIVEN IN BIOCHEMISTRY 36, 3084 - 3094, 1997. JRNL REFERENCE CONTAINS SEQUENCE ERROR IN FIGURE 1 IN T. THERMOPHILUS HISRS, ALA 49 SHOULD BE VAL 49.

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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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growpH: 7 / Details: DESCRIBED IN REFERENCE 1., pH 7.00
Crystal grow
*PLUS
Temperature: 295 K / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-12 mg/mlprotein1drop
250 mMTris Maleate1drop
33 mM1dropMgCl2
40.5 mMdithiothreitol1drop
51 mM1dropNaN3
646 %(w/v)satammonium sulfate1reservoir
710 %(w/v)glycerol1reservoir
850 mMTris Maleate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1997 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.4→12 Å / Num. obs: 39592 / % possible obs: 86.7 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.9 / % possible all: 72.1
Reflection
*PLUS
Num. obs: 17744 / Num. measured all: 39592
Reflection shell
*PLUS
% possible obs: 72.1 % / Rmerge(I) obs: 0.137

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ADJ

1adj


Resolution: 2.4→12 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 57-62 AND 117-120 ARE DISORDERED. OTHER RESIDUES WITH SIDE-CHAIN ATOMS WITH ZERO OCCUPANCY ARE POORLY ORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 899 4.4 %RANDOM
Rwork0.208 ---
obs0.208 17733 86.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.1 Å2 / ksol: 0.44 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.108 Å20 Å20 Å2
2--1.966 Å20 Å2
3----3.073 Å2
Refinement stepCycle: LAST / Resolution: 2.4→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3186 0 5 65 3256
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.264
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4331.5
X-RAY DIFFRACTIONc_mcangle_it3.793
X-RAY DIFFRACTIONc_scbond_it2.4092
X-RAY DIFFRACTIONc_scangle_it5.4894
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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