[English] 日本語
Yorodumi
- PDB-3if5: Crystal Structure Analysis of Mglu -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3if5
TitleCrystal Structure Analysis of Mglu
ComponentsSalt-tolerant glutaminase
KeywordsHYDROLASE / Fragment
Function / homology
Function and homology information


L-glutamine catabolic process / glutamate biosynthetic process / glutaminase / glutaminase activity
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
Biological speciesMicrococcus luteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.44 Å
AuthorsYoshimune, K. / Shirakihara, Y.
Citation
Journal: Febs J. / Year: 2010
Title: Crystal structure of salt-tolerant glutaminase from Micrococcus luteus K-3 in the presence and absence of its product L-glutamate and its activator Tris.
Authors: Yoshimune, K. / Shirakihara, Y. / Wakayama, M. / Yumoto, I.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Crystal structure of a major fragment of the salt-tolerant glutaminase from Micrococcus luteus K-3
Authors: Yoshimune, K. / Shirakihara, Y. / Shiratori, A. / Wakayama, M. / Chantawannakul, P. / Moriguchi, M.
History
DepositionJul 24, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 4, 2009ID: 2DFW
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Salt-tolerant glutaminase


Theoretical massNumber of molelcules
Total (without water)48,3041
Polymers48,3041
Non-polymers00
Water2,072115
1
A: Salt-tolerant glutaminase

A: Salt-tolerant glutaminase


Theoretical massNumber of molelcules
Total (without water)96,6072
Polymers96,6072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6220 Å2
ΔGint-24 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.331, 116.680, 144.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

-
Components

#1: Protein Salt-tolerant glutaminase


Mass: 48303.516 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 700mM Sodium Citrate, 50mM HEPES, 5mM MgCl2, 5% Glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9791, 0.9793, 0.9700
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 26, 2001
RadiationMonochromator: Rotated-inclined double-crystal monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.971
ReflectionResolution: 2.4→36.18 Å / Num. all: 18367 / Num. obs: 17155 / Redundancy: 6.8 % / Biso Wilson estimate: 38.9 Å2

-
Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.44→36.18 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 0.67 / Data cutoff high absF: 6969453 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.256 863 5 %RANDOM
Rwork0.204 ---
obs-17155 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.196 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 110.85 Å2 / Biso mean: 39.072 Å2 / Biso min: 2.42 Å2
Baniso -1Baniso -2Baniso -3
1-4.78 Å20 Å20 Å2
2--9.67 Å20 Å2
3----14.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.44→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 0 0 115 3097
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it2.381.5
X-RAY DIFFRACTIONc_mcangle_it42
X-RAY DIFFRACTIONc_scbond_it3.992
X-RAY DIFFRACTIONc_scangle_it6.492.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 68 5.4 %
Rwork0.233 1196 -
all-1264 -
obs--40 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

+
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