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- PDB-5e3i: Crystal Structure of a Histidyl-tRNA synthetase from Acinetobacte... -

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Basic information

Entry
Database: PDB / ID: 5e3i
TitleCrystal Structure of a Histidyl-tRNA synthetase from Acinetobacter baumannii with bound L-Histidine and ATP
ComponentsHistidine--tRNA ligase
KeywordsLIGASE / SSGCID / histidyl-tRNA synthetase / Acinetobacter baumannii / ATP binding / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


histidine-tRNA ligase / histidyl-tRNA aminoacylation / histidine-tRNA ligase activity / 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
ADENOSINE-5'-TRIPHOSPHATE / HISTIDINE / Histidine--tRNA ligase / Histidine--tRNA ligase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Histidyl-tRNA synthetase from Acinetobacter baumannii with bound L-Histidine and ATP
Authors: SSGCID / Lukacs, C.M. / Dranow, D.M. / Lorimer, D. / Edwards, T.E.
History
DepositionOct 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine--tRNA ligase
B: Histidine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3168
Polymers98,9412
Non-polymers1,3756
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-27 kcal/mol
Surface area31830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.810, 103.070, 246.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Histidine--tRNA ligase / Histidyl-tRNA synthetase


Mass: 49470.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: hisS, ABUW_3376, IOMTU433_3293, RU84_15845 / Plasmid: AcbaC.00063.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A086HW61, UniProt: B0VKR7*PLUS, histidine-tRNA ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: AcbaC.00063.a.B1.PW37682 at 19.5 mg/ml incubated with 3 mM L-Histidine, ATP, and MgCl2, then then mixed 1:1 with MCSG1(e3): 50mM MgCl2, 0.1M Hepes, pH=7.5, 30% PEG-MME550, cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 57675 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 33.7 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.084 / Χ2: 1.016 / Net I/σ(I): 15.55 / Num. measured all: 352039
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.266.30.9040.5333.7926408419641950.58100
2.26-2.320.9330.4454.6125845410841080.484100
2.32-2.390.9490.3685.4425414405240510.401100
2.39-2.460.9690.2936.5824294386338620.319100
2.46-2.540.9750.2477.6723787378537850.269100
2.54-2.630.980.2158.7622821364436430.234100
2.63-2.730.9860.17610.3922153353735360.192100
2.73-2.840.9910.14112.4621138338833880.154100
2.84-2.970.9920.1171520285327232700.12799.9
2.97-3.110.9940.09218.0919119312931250.10199.9
3.11-3.280.9960.0820.4118100298329820.087100
3.28-3.480.9970.06823.2516835281828180.074100
3.48-3.720.9970.05926.0315581266226600.06599.9
3.72-4.020.9970.05427.8614427250625040.05999.9
4.02-4.40.9970.04929.9413159228822870.054100
4.4-4.920.9980.04530.811821208020790.05100
4.92-5.680.9980.04231.4510785184818470.04699.9
5.68-6.960.9980.04231.199332158615860.046100
6.96-9.840.9990.03332.87158125312530.037100
9.84-500.9990.02932.735777366960.03294.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KMM

1kmm


Resolution: 2.2→47.54 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 2000 3.47 %
Rwork0.1647 55669 -
obs0.1661 57669 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.02 Å2 / Biso mean: 41.3577 Å2 / Biso min: 14.9 Å2
Refinement stepCycle: final / Resolution: 2.2→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6031 0 86 460 6577
Biso mean--34.9 41.88 -
Num. residues----786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076267
X-RAY DIFFRACTIONf_angle_d0.918519
X-RAY DIFFRACTIONf_chiral_restr0.05956
X-RAY DIFFRACTIONf_plane_restr0.0051105
X-RAY DIFFRACTIONf_dihedral_angle_d15.8013731
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.25510.24581410.187439064047100
2.2551-2.3160.27061410.183739384079100
2.316-2.38420.24641420.176839744116100
2.3842-2.46110.19831410.171239024043100
2.4611-2.54910.28631410.168539344075100
2.5491-2.65120.22881420.170639624104100
2.6512-2.77180.22041430.173739494092100
2.7718-2.91790.21571410.172639464087100
2.9179-3.10070.21361430.168539654108100
3.1007-3.34010.21011420.172839784120100
3.3401-3.67610.23281450.1640034148100
3.6761-4.20770.17091420.142439894131100
4.2077-5.30020.14321460.137840474193100
5.3002-47.55130.2151500.18754176432699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.02470.6636-0.30792.0506-0.76351.1658-0.11460.1424-0.1194-0.23560.0752-0.45910.00180.14980.03860.2268-0.05150.05010.2613-0.05440.29338.15330.777925.0852
22.07011.5453-0.77181.6862-1.09150.69920.1978-0.04710.0768-0.0777-0.0045-0.1385-0.28350.2295-0.09920.2471-0.01590.00110.1977-0.0130.23130.68531.316832.3753
33.5581-0.9328-0.34894.20640.4731.77690.2692-0.14910.57950.21510.0608-0.1004-0.36540.0264-0.24670.3226-0.01880.10560.2388-0.01520.30152.249428.695557.7818
43.04832.5612.32352.32881.57462.879-1.2551-1.06610.87090.40390.2024-0.401-1.7174-0.42811.10170.3171-0.09840.03350.3652-0.05640.267738.862629.62323.8661
51.59290.812-0.6771.2011-0.32170.8913-0.1036-0.0151-0.3578-0.0232-0.0074-0.22750.19620.03940.0690.2176-0.0113-0.01660.2157-0.00110.256119.58178.140244.1972
60.40260.7715-0.79852.5625-1.37342.2769-0.04630.01220.1469-0.21080.4780.5982-0.1188-0.6188-0.41160.388-0.0093-0.02940.58530.18170.38515.373344.329313.6726
72.02472.00751.99862.00532.00011.9970.2533-0.07210.054-0.2094-0.55210.4890.0238-0.79060.33420.2562-0.0580.0290.3078-0.09260.288721.01778.192144.9674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 282 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 283 through 340 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 341 through 431 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 502 through 502 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 323 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 324 through 430 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 502 through 502 )B0

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