[English] 日本語
Yorodumi
- PDB-3nzt: 2.0 Angstrom Crystal structure of Glutamate--Cysteine Ligase (gsh... -

+
Open data


ID or keywords:

Loading...

-
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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://pdbjlvh1.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