[English] 日本語
Yorodumi
- PDB-3age: Crystal structure of Mglu in its L-glutamate binding form in the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3age
TitleCrystal structure of Mglu in its L-glutamate binding form in the presence of 4.3M NaCl
ComponentsSalt-tolerant glutaminase
KeywordsHYDROLASE / Protein-glutamate complex
Function / homology
Function and homology information


glutaminase / glutaminase activity / glutamine metabolic process
Similarity search - Function
STAS domain / Glutaminase / Glutaminase / Transcription Regulator spoIIAA / STAS domain profile. / STAS domain / STAS domain superfamily / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like ...STAS domain / Glutaminase / Glutaminase / Transcription Regulator spoIIAA / STAS domain profile. / STAS domain / STAS domain superfamily / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Glutaminase
Similarity search - Component
Biological speciesMicrococcus luteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYoshimune, K. / Shirakihara, Y. / Yumoto, I.
CitationJournal: To be Published
Title: Salt-induced conformational change of salt-tolerant glutaminase from Micrococcus luteus K-3
Authors: Yoshimune, K. / Shirakihara, Y. / Yumoto, I.
History
DepositionMar 30, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Salt-tolerant glutaminase
B: Salt-tolerant glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9014
Polymers96,6072
Non-polymers2942
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-45 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.835, 130.933, 73.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Salt-tolerant glutaminase


Mass: 48303.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micrococcus luteus (bacteria) / Strain: K-3 / Gene: Glutaminase / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q4U1A6, glutaminase
#2: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 293 K / Method: microbatch method / pH: 7.5
Details: 10mg/ml protein, 50mM HEPES, 1M ammonium formate, 4.3M NaCl, 0.1M L-glutamate, pH 7.5, Microbatch method, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→73.1 Å / Num. all: 35927 / Num. obs: 35923 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 18.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 6.7 / Num. unique all: 5172 / Rsym value: 0.28 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3if5

3if5


Resolution: 2.6→65.47 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1789 5 %RANDOM
Rwork0.19 34073 --
all-35885 --
obs-35862 100 %-
Solvent computationBsol: 30.856 Å2
Displacement parametersBiso mean: 29.085 Å2
Baniso -1Baniso -2Baniso -3
1-9.451 Å20 Å20 Å2
2---2.856 Å20 Å2
3----6.594 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.6→65.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 20 566 7164
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.6-2.720.3532290.2680.023441399.6
2.72-2.860.3182020.2640.022439699.9
2.86-3.040.3212240.2320.021445699.8
3.04-3.280.2712180.2120.018443099.9
3.28-3.610.2211950.1790.016444599.9
3.61-4.130.2082480.1540.013447399.9

+
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