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- PDB-3rac: Crystal Structure of Histidine--tRNA ligase subunit from Alicyclo... -

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Basic information

Entry
Database: PDB / ID: 3rac
TitleCrystal Structure of Histidine--tRNA ligase subunit from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446.
ComponentsHistidine-tRNA ligaseHistidine—tRNA ligase
KeywordsLIGASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / PSI-BIO / PROTEIN STRUCTURE INITIATIVE / CENTER FOR STRUCTURAL GENOMICS / LPHA-BETA-ALPHA fold and LPHA fold / TRANSFERASE / CYTOSOL
Function / homology
Function and homology information


histidine-tRNA ligase / ligase activity / cytoplasm
Similarity search - Function
Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / (2S)-2-hydroxybutanedioic acid / Histidine--tRNA ligase
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.301 Å
AuthorsWu, R. / Bedean, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Strucutre of Histidine--tRNA ligase subunit from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446.
Authors: Wu, R. / Bedean, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMar 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references / Structure summary
Revision 1.2Sep 9, 2020Group: Database references / Derived calculations / Structure summary
Category: pdbx_struct_conn_angle / struct ...pdbx_struct_conn_angle / struct / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct.title / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4137
Polymers41,0211
Non-polymers3926
Water1,62190
1
A: Histidine-tRNA ligase
hetero molecules

A: Histidine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,82714
Polymers82,0422
Non-polymers78512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7440 Å2
ΔGint-65 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.276, 69.276, 177.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-406-

ACY

21A-406-

ACY

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histidine-tRNA ligase / Histidine—tRNA ligase / ATP PHOSPHORIBOSYLTRANSFERASE REGULATORY SUBUNIT


Mass: 41021.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
Strain: DSM 446 / Gene: Aaci_0923 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 MAGIC / References: UniProt: C8WUX4, histidine-tRNA ligase

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Non-polymers , 5 types, 96 molecules

#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.045M DL-Malic acid, 0.075M sodium formate 0.1M Na-Hepes 7.0, 10% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 11, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 33816 / % possible obs: 99.2 % / Redundancy: 7.8 % / Biso Wilson estimate: 51.2 Å2 / Rsym value: 0.105 / Net I/σ(I): 24.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 965 / Rsym value: 0.868 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.301→37.744 Å / SU ML: 0.36 / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2389 1720 5.09 %
Rwork0.1893 --
obs0.1917 33816 92.25 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.932 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.5502 Å20 Å2-0 Å2
2--8.5502 Å20 Å2
3----17.1004 Å2
Refinement stepCycle: LAST / Resolution: 2.301→37.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 25 90 2748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082709
X-RAY DIFFRACTIONf_angle_d1.0943670
X-RAY DIFFRACTIONf_dihedral_angle_d14.962993
X-RAY DIFFRACTIONf_chiral_restr0.073400
X-RAY DIFFRACTIONf_plane_restr0.004487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.38330.3441680.29072777X-RAY DIFFRACTION79
2.3833-2.47870.30261550.2532862X-RAY DIFFRACTION83
2.4787-2.59150.26041830.23122957X-RAY DIFFRACTION86
2.5915-2.72810.29411870.2353105X-RAY DIFFRACTION90
2.7281-2.89890.30461790.22453242X-RAY DIFFRACTION93
2.8989-3.12260.25841670.19993348X-RAY DIFFRACTION96
3.1226-3.43670.2491770.19563419X-RAY DIFFRACTION98
3.4367-3.93350.23521920.17623435X-RAY DIFFRACTION99
3.9335-4.95410.19031430.1443522X-RAY DIFFRACTION100
4.9541-37.74930.20271690.18753429X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 35.0197 Å / Origin y: 4.6679 Å / Origin z: -3.7711 Å
111213212223313233
T0.3659 Å2-0.0418 Å20.0218 Å2-0.213 Å2-0.0063 Å2--0.2797 Å2
L1.0911 °2-0.7061 °2-0.4535 °2-0.4953 °20.3615 °2--1.5596 °2
S-0.1122 Å °0.0132 Å °-0.0675 Å °0.0443 Å °0.0356 Å °0.0352 Å °0.3208 Å °0.115 Å °0 Å °
Refinement TLS groupSelection details: chain A resid 15:365

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