[English] 日本語
Yorodumi
- PDB-7f79: Crystal structure of glutamate dehydrogenase 3 from Candida albic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f79
TitleCrystal structure of glutamate dehydrogenase 3 from Candida albicans in complex with alpha-ketoglutarate and NADPH
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / Candida albicans / Yeast-to-hyphal transition / Glutamate dehydrogenase / Conformational change
Function / homology
Function and homology information


glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / nucleotide binding / cytosol
Similarity search - Function
: / Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase ...: / Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / Chem-NDP / Glutamate dehydrogenase
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, N. / Wang, W. / Zeng, X. / Liu, M. / Li, M. / Li, C. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government1808085MC53 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of glutamate dehydrogenase 3 from Candida albicans.
Authors: Li, N. / Wang, W. / Zeng, X. / Liu, M. / Li, M. / Li, C. / Wang, M.
History
DepositionJun 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate dehydrogenase
B: Glutamate dehydrogenase
C: Glutamate dehydrogenase
D: Glutamate dehydrogenase
E: Glutamate dehydrogenase
F: Glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,04523
Polymers317,2356
Non-polymers5,81017
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33530 Å2
ΔGint-48 kcal/mol
Surface area85250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.279, 155.224, 98.807
Angle α, β, γ (deg.)90.000, 95.500, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 21 or resid 23...
21(chain B and (resid 3 through 21 or resid 23...
31(chain C and (resid 3 through 21 or resid 23...
41(chain D and (resid 3 through 21 or resid 23...
51(chain E and (resid 3 through 21 or resid 23...
61(chain F and (resid 3 through 21 or resid 23...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLUGLU(chain A and (resid 3 through 21 or resid 23...AA3 - 2123 - 41
12SERSERSERSER(chain A and (resid 3 through 21 or resid 23...AA23 - 42243 - 442
13LEULEUPHEPHE(chain A and (resid 3 through 21 or resid 23...AA430 - 456450 - 476
14NDPNDPHOHHOH(chain A and (resid 3 through 21 or resid 23...AG - X501 - 601
21LEULEUGLUGLU(chain B and (resid 3 through 21 or resid 23...BB3 - 2123 - 41
22SERSERSERSER(chain B and (resid 3 through 21 or resid 23...BB23 - 42243 - 442
23LEULEUPHEPHE(chain B and (resid 3 through 21 or resid 23...BB430 - 456450 - 476
24NDPNDPHOHHOH(chain B and (resid 3 through 21 or resid 23...BJ - Y501 - 601
31LEULEUGLUGLU(chain C and (resid 3 through 21 or resid 23...CC3 - 2123 - 41
32SERSERSERSER(chain C and (resid 3 through 21 or resid 23...CC23 - 42243 - 442
33LEULEUPHEPHE(chain C and (resid 3 through 21 or resid 23...CC430 - 456450 - 476
34NDPNDPHOHHOH(chain C and (resid 3 through 21 or resid 23...CM - Z501 - 601
41LEULEUGLUGLU(chain D and (resid 3 through 21 or resid 23...DD3 - 2123 - 41
42SERSERSERSER(chain D and (resid 3 through 21 or resid 23...DD23 - 42243 - 442
43LEULEUPHEPHE(chain D and (resid 3 through 21 or resid 23...DD430 - 456450 - 476
44NDPNDPHOHHOH(chain D and (resid 3 through 21 or resid 23...DO - AA501 - 601
51LEULEUGLUGLU(chain E and (resid 3 through 21 or resid 23...EE3 - 2123 - 41
52SERSERSERSER(chain E and (resid 3 through 21 or resid 23...EE23 - 42243 - 442
53LEULEUPHEPHE(chain E and (resid 3 through 21 or resid 23...EE430 - 456450 - 476
54NDPNDPHOHHOH(chain E and (resid 3 through 21 or resid 23...ES - BA501 - 601
61LEULEUGLUGLU(chain F and (resid 3 through 21 or resid 23...FF3 - 2123 - 41
62SERSERSERSER(chain F and (resid 3 through 21 or resid 23...FF23 - 42243 - 442
63LEULEUPHEPHE(chain F and (resid 3 through 21 or resid 23...FF430 - 456450 - 476
64NDPNDPHOHHOH(chain F and (resid 3 through 21 or resid 23...FV - CA501 - 601

-
Components

#1: Protein
Glutamate dehydrogenase


Mass: 52872.508 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / Gene: GDH3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D8PMH8
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M DL-Malic acid, pH 7.0, and 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 79980 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.098 / Rrim(I) all: 0.185 / Χ2: 0.873 / Net I/σ(I): 3.8 / Num. measured all: 274007
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.83.40.98479500.5280.621.1670.74698.7
2.8-2.913.40.73579770.6610.4630.8710.77398.7
2.91-3.043.40.57380370.7570.3620.680.83899
3.04-3.23.30.40279720.8520.2590.480.90298.6
3.2-3.43.40.29778140.9190.1870.3520.98396.3
3.4-3.663.60.22280650.9460.1370.2611.00399.5
3.66-4.033.50.15780790.9680.0980.1861.09599.3
4.03-4.623.40.11480570.9810.0730.1361.02999.1
4.62-5.813.50.09579410.9850.060.1130.83997.5
5.81-503.50.05480880.9850.0340.0640.52198

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XVX

5xvx


Resolution: 2.7→44.8 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 3325 5 %
Rwork0.1988 63227 -
obs0.2013 66552 84.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.47 Å2 / Biso mean: 42.517 Å2 / Biso min: 13.38 Å2
Refinement stepCycle: final / Resolution: 2.7→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20836 0 378 326 21540
Biso mean--40.99 31.11 -
Num. residues----2723
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12826X-RAY DIFFRACTION8.89TORSIONAL
12B12826X-RAY DIFFRACTION8.89TORSIONAL
13C12826X-RAY DIFFRACTION8.89TORSIONAL
14D12826X-RAY DIFFRACTION8.89TORSIONAL
15E12826X-RAY DIFFRACTION8.89TORSIONAL
16F12826X-RAY DIFFRACTION8.89TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.740.3627730.29931315138842
2.74-2.780.4034890.26141455154447
2.78-2.820.2887880.26831664175253
2.82-2.870.3358930.26461795188859
2.87-2.920.25681010.27041958205962
2.92-2.970.3111050.27762120222569
2.97-3.030.3681080.29322312242073
3.03-3.090.29841180.27082437255577
3.09-3.160.3141250.2652501262681
3.16-3.230.34431280.27182520264881
3.23-3.310.30231300.24962960309093
3.31-3.40.30831730.23743060323399
3.4-3.50.27841770.22443068324599
3.5-3.610.28521900.21883082327299
3.61-3.740.23561640.20183138330299
3.74-3.890.22271370.1953126326399
3.89-4.070.24521620.18333117327999
4.07-4.290.2171890.16923091328099
4.29-4.550.22371730.15933099327299
4.55-4.90.19821670.15562926309394
4.9-5.40.20371520.16313152330499
5.4-6.180.21491890.172631283317100
6.18-7.780.22121500.17033138328899
7.78-44.80.17711440.14983065320995

+
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