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- PDB-7f77: Crystal structure of glutamate dehydrogenase 3 from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 7f77
TitleCrystal structure of glutamate dehydrogenase 3 from Candida albicans
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
Glutamate dehydrogenase
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.086 Å
AuthorsLi, N. / Wang, W. / Zeng, X. / Liu, M. / Li, M. / Li, C. / Wang, M.
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


Theoretical massNumber of molelcules
Total (without water)158,6183
Polymers158,6183
Non-polymers00
Water30617
1
A: Glutamate dehydrogenase
B: Glutamate dehydrogenase
C: Glutamate dehydrogenase

A: Glutamate dehydrogenase
B: Glutamate dehydrogenase
C: Glutamate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)317,2356
Polymers317,2356
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)94.542, 94.542, 334.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 173 or resid 193...
21(chain B and (resid 6 through 384 or resid 395 through 424 or resid 430 through 456))
31(chain C and (resid 6 through 173 or resid 193 through 277 or resid 287 through 456))

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
11GLUGLUASNASN(chain A and (resid 6 through 173 or resid 193...AA6 - 17326 - 193
12PROPROPHEPHE(chain A and (resid 6 through 173 or resid 193...AA193 - 277213 - 297
13SERSERGLUGLU(chain A and (resid 6 through 173 or resid 193...AA287 - 384307 - 404
14THRTHRGLUGLU(chain A and (resid 6 through 173 or resid 193...AA395 - 424415 - 444
15LEULEUPHEPHE(chain A and (resid 6 through 173 or resid 193...AA430 - 456450 - 476
21GLUGLUGLUGLU(chain B and (resid 6 through 384 or resid 395 through 424 or resid 430 through 456))BB6 - 38426 - 404
22THRTHRGLUGLU(chain B and (resid 6 through 384 or resid 395 through 424 or resid 430 through 456))BB395 - 424415 - 444
23LEULEUPHEPHE(chain B and (resid 6 through 384 or resid 395 through 424 or resid 430 through 456))BB430 - 456450 - 476
31GLUGLUASNASN(chain C and (resid 6 through 173 or resid 193 through 277 or resid 287 through 456))CC6 - 17326 - 193
32PROPROPHEPHE(chain C and (resid 6 through 173 or resid 193 through 277 or resid 287 through 456))CC193 - 277213 - 297
33SERSERPHEPHE(chain C and (resid 6 through 173 or resid 193 through 277 or resid 287 through 456))CC287 - 456307 - 476

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Components

#1: Protein Glutamate dehydrogenase


Mass: 52872.508 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / Gene: GDH3 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1D8PMH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M Sodium Malonate, pH 3.5, and 17% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.08→50 Å / Num. obs: 26983 / % possible obs: 93.3 % / Redundancy: 8 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.046 / Rrim(I) all: 0.142 / Χ2: 0.844 / Net I/σ(I): 4.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.218.31.0526820.720.3451.110.58994.9
3.21-3.348.30.72827000.8350.240.770.62996.3
3.34-3.498.10.56527060.8920.190.5980.74495
3.49-3.687.80.43926800.90.1520.4670.85494.9
3.68-3.917.70.33526700.9450.1160.3560.97694.4
3.91-4.218.30.20626740.9770.0690.2180.97692.9
4.21-4.638.10.1426620.9890.0480.1491.06392.6
4.63-5.37.70.1226810.9880.0430.1281.0391.8
5.3-6.678.10.10227310.990.0340.1080.89392.6
6.67-507.40.06427970.9950.0230.0690.71588

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XVX

5xvx


Resolution: 3.086→43.518 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2903 1154 4.75 %
Rwork0.2409 23132 -
obs0.2433 24286 83.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.7 Å2 / Biso mean: 59.1094 Å2 / Biso min: 13.39 Å2
Refinement stepCycle: final / Resolution: 3.086→43.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9716 0 0 17 9733
Biso mean---29.6 -
Num. residues----1269
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5713X-RAY DIFFRACTION9.624TORSIONAL
12B5713X-RAY DIFFRACTION9.624TORSIONAL
13C5713X-RAY DIFFRACTION9.624TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.086-3.22640.3975660.3036128738
3.2264-3.39650.33871280.2851274481
3.3965-3.60920.29681830.2723309792
3.6092-3.88770.34831480.2683318093
3.8877-4.27860.30171560.2357317193
4.2786-4.8970.27011530.2126319492
4.897-6.16690.25221620.2282321392
6.1669-43.5180.26251580.2233324687

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