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- PDB-3nzt: 2.0 Angstrom Crystal structure of Glutamate--Cysteine Ligase (gsh... -

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Basic information

Entry
Database: PDB / ID: 3nzt
Title2.0 Angstrom Crystal structure of Glutamate--Cysteine Ligase (gshA) ftom Francisella tularensis in Complex with AMP
ComponentsGlutamate--cysteine ligase
KeywordsLIGASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha and beta proteins
Function / homology
Function and homology information


glutamate-cysteine ligase / glutamate-cysteine ligase activity / glutathione biosynthetic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Glutamate--cysteine ligase, monofunctional / Glutamate--cysteine ligase / Glutamate-cysteine ligase / Creatine Kinase; Chain A, domain 2 - #20 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Glutamate--cysteine ligase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.0 Angstrom Crystal structure of Glutamate--Cysteine Ligase (gshA) ftom Francisella tularensis in Complex with AMP.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F.
History
DepositionJul 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,12913
Polymers59,7251
Non-polymers1,40412
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.849, 89.849, 151.468
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Glutamate--cysteine ligase


Mass: 59724.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT_0367c, gshA / Plasmid: pMSCG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 (Magic) / References: UniProt: Q5NHS8, glutamate-cysteine ligase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.96 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: protein: 7.3 mg/mL, 0.5M Sodium chloride, Tris-HCl (pH 8.3), 1mM AMPPNP, 1mM Magnesium chloride, screen: ClassicsII, drop A2, 0.1M Sodium acetate (pH 4.5), 2M Ammonium sulphate, Cryo: 1.8M ...Details: protein: 7.3 mg/mL, 0.5M Sodium chloride, Tris-HCl (pH 8.3), 1mM AMPPNP, 1mM Magnesium chloride, screen: ClassicsII, drop A2, 0.1M Sodium acetate (pH 4.5), 2M Ammonium sulphate, Cryo: 1.8M Ammonium sulphate, 25% Sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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: Mar 8, 2010 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 46618 / Num. obs: 46618 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 25.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2296 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D32

2d32


Resolution: 2→29.41 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.778 / SU ML: 0.087 / Isotropic thermal model: Individually refined / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19598 2351 5 %RANDOM
Rwork0.1639 ---
all0.16548 44206 --
obs0.16548 44206 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20.42 Å2-0 Å2
2--0.84 Å2-0 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 2→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3977 0 78 328 4383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224267
X-RAY DIFFRACTIONr_bond_other_d0.0010.022896
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9915782
X-RAY DIFFRACTIONr_angle_other_deg0.84837099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1495526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07125.098204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.4815792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7791524
X-RAY DIFFRACTIONr_chiral_restr0.090.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02825
X-RAY DIFFRACTIONr_mcbond_it0.8521.52577
X-RAY DIFFRACTIONr_mcbond_other0.2441.51037
X-RAY DIFFRACTIONr_mcangle_it1.56424174
X-RAY DIFFRACTIONr_scbond_it2.67431690
X-RAY DIFFRACTIONr_scangle_it4.3244.51608
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 182 -
Rwork0.205 3222 -
obs-3222 99.44 %
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)
11.80670.34820.23111.43670.67131.6361-0.0668-0.10640.1049-0.1516-0.01970.0796-0.10650.0170.08650.0230.0029-0.01670.0274-0.02220.030544.679433.871723.3575
22.2311.82690.5133.02090.4120.68560.0092-0.0324-0.1560.0130.0694-0.25350.06980.2738-0.07860.06730.0039-0.02360.1618-0.02190.098161.159730.239728.5789
31.24350.84950.25152.85810.82952.3707-0.07060.0775-0.237-0.21630.01790.01670.1717-0.0390.05280.0945-0.0168-0.00620.0179-0.0320.088540.970717.550814.1645
43.08560.5493-0.36521.21360.09681.72550.1106-0.39940.1645-0.1213-0.07590.1665-0.212-0.1078-0.03470.11260.0178-0.03510.088-0.06470.123743.080341.720330.4883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 217
2X-RAY DIFFRACTION2A218 - 309
3X-RAY DIFFRACTION3A310 - 429
4X-RAY DIFFRACTION4A430 - 501

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