[English] 日本語
Yorodumi
- PDB-9zpg: Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9zpg
TitleCrystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis (Apo)
ComponentsGlutamate--tRNA ligase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Glutamate--tRNA ligase (GltX)
Function / homology
Function and homology information


glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Glutamate-tRNA ligase, bacterial/mitochondrial / Glutamyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Aminoacyl-tRNA synthetase, class I, anticodon-binding / Anticodon binding domain / : / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain ...Glutamate-tRNA ligase, bacterial/mitochondrial / Glutamyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Aminoacyl-tRNA synthetase, class I, anticodon-binding / Anticodon binding domain / : / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Glutamate--tRNA ligase
Similarity search - Component
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis (Apo)
Authors: Seibold, S. / Lovell, S. / Enayati, P. / Battaile, K.P.
History
DepositionDec 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,24216
Polymers117,7712
Non-polymers1,47114
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-190 kcal/mol
Surface area44050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.557, 53.602, 127.962
Angle α, β, γ (deg.)90.00, 108.19, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glutamate--tRNA ligase / Glutamyl-tRNA synthetase / GluRS


Mass: 58885.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella catarrhalis (bacteria) / Gene: gltX, AO370_0559 / Plasmid: MocaA.01348.a.UX11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AB36DQE3, glutamate-tRNA ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Grid Salt HT B10: 3.0M Ammonium Sulfate 0.1M HEPES pH 7.0, MocaA.01348.a.UX11.PS38771 at 26.6 mg/mL. plate 20153 B10 drop 2, Puck: PSL-1810, Cryo: 2.5 M ammonium sulfate.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 4, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.75→47.07 Å / Num. obs: 35110 / % possible obs: 99.6 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.06 / Rrim(I) all: 0.16 / Χ2: 0.99 / Net I/σ(I): 10 / Num. measured all: 239953
Reflection shellResolution: 2.75→2.88 Å / % possible obs: 99.4 % / Redundancy: 7.2 % / Rmerge(I) obs: 1.31 / Num. measured all: 33376 / Num. unique obs: 4621 / CC1/2: 0.634 / Rpim(I) all: 0.519 / Rrim(I) all: 1.41 / Χ2: 1.02 / Net I/σ(I) obs: 1.5

-
Processing

Software
NameVersionClassification
PHENIX(2.0_5904: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→47.07 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2613 1709 4.87 %
Rwork0.2154 --
obs0.2177 35096 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7659 0 80 0 7739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047911
X-RAY DIFFRACTIONf_angle_d0.58710760
X-RAY DIFFRACTIONf_dihedral_angle_d16.5972859
X-RAY DIFFRACTIONf_chiral_restr0.0391186
X-RAY DIFFRACTIONf_plane_restr0.0061378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.830.41811430.34852769X-RAY DIFFRACTION99
2.83-2.920.32441280.29522729X-RAY DIFFRACTION99
2.92-3.030.33911410.29152744X-RAY DIFFRACTION99
3.03-3.150.35061570.29382788X-RAY DIFFRACTION99
3.15-3.290.32851280.28532746X-RAY DIFFRACTION100
3.29-3.460.29261480.25022751X-RAY DIFFRACTION99
3.46-3.680.27341610.22562759X-RAY DIFFRACTION100
3.68-3.970.24991440.21042772X-RAY DIFFRACTION99
3.97-4.360.23941510.18292786X-RAY DIFFRACTION100
4.36-4.990.20821300.16782786X-RAY DIFFRACTION99
5-6.290.25721320.20212823X-RAY DIFFRACTION99
6.29-47.070.20661460.17412934X-RAY DIFFRACTION100
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)
15.58830.3214-1.50541.0132-0.73687.00740.27940.0248-0.07130.0829-0.0564-0.07620.04870.3871-0.17710.32990.0807-0.0830.27870.02410.4409-10.57320.3774-40.144
20.520.0972-0.0841.2832-0.76431.7628-0.0330.1178-0.00140.02640.0346-0.0161-0.04480.1095-0.00190.28020.0061-0.08350.4064-0.01210.4669-14.438130.2505-54.1488
30.5492-0.14050.29731.82010.24362.6972-0.063-0.04050.0490.16570.07440.1692-0.088-0.1969-0.01460.4616-0.0084-0.02690.35810.04130.5763-25.676628.1998-21.6359
43.3294-3.2295-1.41644.5598-0.90977.28650.1283-0.0235-0.0123-0.2184-0.09830.1709-0.30360.1533-0.060.401-0.1005-0.09180.39440.07110.4685-12.982614.491128.1606
51.7671-0.1361-0.15661.764-0.35773.51190.0946-0.3506-0.04620.1158-0.10090.2831-0.1096-0.2148-0.00170.3938-0.0478-0.03570.54260.01320.4966-21.38827.015744.7978
60.3974-0.050.47940.3387-0.09346.2329-0.0766-0.17430.15170.47340.0324-0.0951-1.3186-0.11260.04360.9760.0218-0.11270.46220.02470.6045-18.148728.141918.068
72.18310.168-1.2611.9624-0.23976.79810.0618-0.3036-0.18850.2248-0.09930.10640.4597-1.01660.05150.585-0.1299-0.07610.61780.08550.5188-34.84188.65315.1769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 271 )
3X-RAY DIFFRACTION3chain 'A' and (resid 272 through 498 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 66 )
5X-RAY DIFFRACTION5chain 'B' and (resid 67 through 252 )
6X-RAY DIFFRACTION6chain 'B' and (resid 253 through 343 )
7X-RAY DIFFRACTION7chain 'B' and (resid 344 through 497 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more