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- PDB-9z2x: Crystal structure of Glutamate-tRNA synthetase GluRS from Chlamyd... -

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Basic information

Entry
Database: PDB / ID: 9z2x
TitleCrystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae (Orthorhombic C form)
ComponentsGlutamate--tRNA ligase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / TRANSFERASE / Glutamate-tRNA synthetase / Chlamydia pneumoniae in complex with ATP
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 speciesChlamydia pneumoniae (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 synthetase GluRS from Chlamydia pneumoniae (Orthorhombic C form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionNov 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6744
Polymers60,5681
Non-polymers1063
Water00
1
A: Glutamate--tRNA ligase
hetero molecules

A: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3498
Polymers121,1362
Non-polymers2136
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4430 Å2
ΔGint-86 kcal/mol
Surface area42950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.368, 135.411, 111.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 60568.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia pneumoniae (bacteria) / Gene: gltX, CPn_0560, CP_0190, CpB0582 / Plasmid: ChpnA.01348.a.UX11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Z7Z3, glutamate-tRNA ligase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestN
Has protein modificationN

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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: 3.26 Å3/Da / Density % sol: 62.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M NaCH3COO/CH3COOH pH 5.0, 2% PEG 4000, 15% MPD. ChpnA.01348.a.UX11.PS38780 at 8 mg/mL. 2 mM ATP added to the protein prior to crystallization. plate 20340 E8 drop 1, Puck: PSL-1216, Cryo: ...Details: 0.1M NaCH3COO/CH3COOH pH 5.0, 2% PEG 4000, 15% MPD. ChpnA.01348.a.UX11.PS38780 at 8 mg/mL. 2 mM ATP added to the protein prior to crystallization. plate 20340 E8 drop 1, Puck: PSL-1216, Cryo: 25% MPD + 75% crystallant

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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: Sep 20, 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→47.29 Å / Num. obs: 20966 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.083 / Rrim(I) all: 0.227 / Χ2: 1.01 / Net I/σ(I): 7.4 / Num. measured all: 156349
Reflection shellResolution: 2.75→2.9 Å / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 1.583 / Num. measured all: 23671 / Num. unique obs: 2996 / CC1/2: 0.756 / Rpim(I) all: 0.599 / Rrim(I) all: 1.695 / Χ2: 1.01 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX2.0_5855refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→47.29 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2648 1030 4.93 %
Rwork0.2194 --
obs0.2217 20912 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 3 0 3855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053957
X-RAY DIFFRACTIONf_angle_d0.75363
X-RAY DIFFRACTIONf_dihedral_angle_d17.2651457
X-RAY DIFFRACTIONf_chiral_restr0.04572
X-RAY DIFFRACTIONf_plane_restr0.006685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.890.38241190.33782799X-RAY DIFFRACTION100
2.9-3.080.39361590.32382805X-RAY DIFFRACTION100
3.08-3.310.32821460.26562792X-RAY DIFFRACTION100
3.31-3.650.31791570.24132812X-RAY DIFFRACTION100
3.65-4.170.2291420.20112846X-RAY DIFFRACTION100
4.17-5.260.24631360.17822877X-RAY DIFFRACTION100
5.26-47.290.20641710.18762951X-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)
12.45880.3275-0.16872.5716-0.67913.5703-0.2587-0.61650.40940.32780.3718-0.2103-0.03270.0119-0.1980.40450.05030.0280.6502-0.08660.4349-16.0416-28.63183.1749
21.83250.9262-0.19741.5524-0.25023.31990.1205-0.4536-0.15570.1142-0.1545-0.18050.20180.28350.01850.56490.10650.02321.1135-0.04970.5821-16.6218-35.789722.0341
32.0419-0.2981-2.03790.4125-0.02834.77230.05780.03210.06230.08910.10510.14290.1432-0.8612-0.15590.4046-0.0198-0.02040.53460.03480.4223-21.332-36.7685-9.0874
41.2861-0.03340.03092.9679-1.77943.3664-0.0965-0.3382-0.10650.11710.116-0.0820.1454-0.1435-0.03330.35270.04-0.01170.55380.01750.40086.0438-49.7008-10.732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 233 )
3X-RAY DIFFRACTION3chain 'A' and (resid 234 through 344 )
4X-RAY DIFFRACTION4chain 'A' and (resid 345 through 504 )

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