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- PDB-7f79: Crystal structure of glutamate dehydrogenase 3 from Candida albic... -

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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 / 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 ...Glutamate dehydrogenase / 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 domain superfamily
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.32 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

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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

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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

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