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- PDB-1htt: HISTIDYL-TRNA SYNTHETASE -

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Basic information

Entry
Database: PDB / ID: 1htt
TitleHISTIDYL-TRNA SYNTHETASE
ComponentsHISTIDYL-TRNA SYNTHETASE
KeywordsCOMPLEX (TRNA SYNTHETASE/HIS-ADENYLATE) / COMPLEX (TRNA SYNTHETASE-HIS-ADENYLATE) / AMINOACYL-TRNA SYNTHASE / LIGASE / SYNTHETASE / COMPLEX (TRNA SYNTHETASE-HIS-ADENYLATE) complex
Function / homology
Function and homology information


histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
Histidyl-anticodon-binding / 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 ...Histidyl-anticodon-binding / 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
ADENOSINE MONOPHOSPHATE / HISTIDINE / Histidine--tRNA ligase / Histidine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR, DENSITY AVERAGING / Resolution: 2.6 Å
AuthorsArnez, J.G. / Harris, D.C. / Mitschler, A. / Rees, B. / Francklyn, C.S. / Moras, D.
Citation
Journal: EMBO J. / Year: 1995
Title: Crystal structure of histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate.
Authors: Arnez, J.G. / Harris, D.C. / Mitschler, A. / Rees, B. / Francklyn, C.S. / Moras, D.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization of Histidyl-tRNA Synthetase from Escherichia Coli
Authors: Francklyn, C. / Harris, D. / Moras, D.
#2: Journal: J.Biol.Chem. / Year: 1985
Title: Primary Structure of Histidine-tRNA Synthetase and Characterization of Hiss Transcripts
Authors: Freedman, R. / Gibson, B. / Donovan, D. / Biemann, K. / Eisenbeis, S. / Parker, J. / Schimmel, P.
History
DepositionMar 9, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 7, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_conn / 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 / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)189,83012
Polymers187,8164
Non-polymers2,0148
Water2,828157
1
A: HISTIDYL-TRNA SYNTHETASE
B: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9156
Polymers93,9082
Non-polymers1,0074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-24 kcal/mol
Surface area28980 Å2
MethodPISA
2
C: HISTIDYL-TRNA SYNTHETASE
D: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9156
Polymers93,9082
Non-polymers1,0074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-25 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.400, 110.700, 108.700
Angle α, β, γ (deg.)115.00, 97.40, 90.00
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2, -0.007, -0.98), (-0.002, -1, 0.007), (-0.98, 0.003, 0.2)2.411, 9.168, 1.967
2given(-1, -0.001, 0.002), (-0.001, 1), (-0.002, -1)-0.027, -9.354, -0.044
3given(0.198, 0.008, 0.98), (-0.003, -1, 0.008), (0.98, -0.004, -0.198)-2.428, -0.182, -2.045

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Components

#1: Protein
HISTIDYL-TRNA SYNTHETASE / HISTIDINE-TRNA LIGASE


Mass: 46954.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Plasmid: PHRS-7 / Gene (production host): HISS / Production host: Escherichia coli (E. coli)
References: UniProt: P04804, UniProt: P60906*PLUS, histidine-tRNA ligase
#2: Chemical
ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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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: 3.49 Å3/Da / Density % sol: 68 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein complex1drop
20.1 MTris-HCl1reservoir
30.5 M1reservoirNaCl
410 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 9, 1994
RadiationMonochromator: GRAPHITE HUBER FLAT #151 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→26 Å / Num. obs: 54820 / % possible obs: 69.4 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 2.8 / % possible all: 55.7

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MARXDSdata reduction
Agrovatadata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR, DENSITY AVERAGING / Resolution: 2.6→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.327 -6 %
Rwork0.246 --
obs0.246 52961 69.9 %
Displacement parametersBiso mean: 33 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11250 0 132 157 11539
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.925
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.07
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.209
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.072
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.209

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