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- PDB-1ady: HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDYL-ADENYLATE -

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Basic information

Entry
Database: PDB / ID: 1ady
TitleHISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDYL-ADENYLATE
ComponentsHISTIDYL-TRNA SYNTHETASEHistidine—tRNA ligase
KeywordsTRNA SYNTHETASE / HISTIDYL-ADENYLATE / AMINO ACID
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
HISTIDYL-ADENOSINE MONOPHOSPHATE / Histidine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCusack, S. / Aberg, A.
CitationJournal: 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
DepositionFeb 19, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTIDYL-TRNA SYNTHETASE
B: HISTIDYL-TRNA SYNTHETASE
C: HISTIDYL-TRNA SYNTHETASE
D: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,82512
Polymers188,5044
Non-polymers2,3228
Water0
1
A: HISTIDYL-TRNA SYNTHETASE
B: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4136
Polymers94,2522
Non-polymers1,1614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9620 Å2
ΔGint-47 kcal/mol
Surface area34100 Å2
MethodPISA
2
C: HISTIDYL-TRNA SYNTHETASE
D: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4136
Polymers94,2522
Non-polymers1,1614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-47 kcal/mol
Surface area34210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.300, 214.700, 49.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.947217, 0.308044, 0.088825), (0.319919, 0.926198, 0.199524), (-0.020807, 0.217409, -0.975859)78.67346, -18.40144, 47.55746
2given(0.996759, -0.077357, -0.022076), (-0.080225, -0.976175, -0.201608), (-0.005955, 0.202725, -0.979218)3.13186, 127.888, 47.89478
3given(-0.969574, 0.243148, -0.028375), (-0.241482, -0.969008, -0.052061), (-0.040154, -0.043625, 0.998241)84.83533, 130.34251, 3.61826

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Components

#1: Protein
HISTIDYL-TRNA SYNTHETASE / Histidine—tRNA ligase


Mass: 47125.918 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: HISTIDYL-ADENYLATE PRODUCED ENZYMATICALLY IN THE CRYSTAL IS PRESENT IN THE ACTIVE SITE
Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P56194, histidine-tRNA ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HAM / HISTIDYL-ADENOSINE MONOPHOSPHATE


Mass: 484.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H21N8O8P

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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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growpH: 7 / Details: pH 7.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlhistidyl-tRNA1drop
24.3 mg/mltRNAHis1drop
33-10 mM1dropMgCl2
41 mM1dropNaN3
515 %(v/v)ammonium sulphate1drop
6100 mMbis-tris propane1drop
750 %satammonium sulphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 31, 1995 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 32840 / % possible obs: 65 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 5
Reflection
*PLUS
Num. measured all: 85481
Reflection shell
*PLUS
% possible obs: 30 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HISTIDYL-TRNA SYNTHETASE

Resolution: 2.8→20 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.3 -5 %RANDOM
Rwork0.26 ---
obs0.26 32813 65 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13236 0 152 0 13388
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.184
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 1632
Solvent computation
*PLUS
Displacement parameters
*PLUS

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