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- PDB-8s3g: Atomic structure of truncated worm GdH -

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Basic information

Entry
Database: PDB / ID: 8s3g
TitleAtomic structure of truncated worm GdH
ComponentsGlutamate dehydrogenase
KeywordsSTRUCTURAL PROTEIN / GdH Enzyme worm Xray
Function / homology
Function and homology information


glutamate dehydrogenase (NAD+) activity / L-glutamate catabolic process / nucleotide binding / mitochondrion
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 speciesHeligmosomoides polygyrus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsMourao, A. / Sattler, M. / Geerlof, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Atomic structure of truncated worm GdH
Authors: Mourao, A. / Sattler, M. / Geerlof, A.
History
DepositionFeb 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate dehydrogenase
B: Glutamate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)118,4172
Polymers118,4172
Non-polymers00
Water3,135174
1
A: Glutamate dehydrogenase

A: Glutamate dehydrogenase

A: Glutamate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)177,6263
Polymers177,6263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area9560 Å2
ΔGint-53 kcal/mol
Surface area58710 Å2
2
B: Glutamate dehydrogenase

B: Glutamate dehydrogenase

B: Glutamate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)177,6263
Polymers177,6263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area9390 Å2
ΔGint-51 kcal/mol
Surface area58570 Å2
Unit cell
Length a, b, c (Å)151.245, 151.245, 146.043
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z

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Components

#1: Protein Glutamate dehydrogenase


Mass: 59208.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heligmosomoides polygyrus (invertebrata)
Gene: HPBE_LOCUS9300 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A183FP08
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 4.07 Å3/Da / Density % sol: 69.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M acetic acid ph 5.5 20% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.29→97.51 Å / Num. obs: 167056 / % possible obs: 99.35 % / Redundancy: 5.2 % / Biso Wilson estimate: 39.78 Å2 / CC1/2: 0.974 / Net I/σ(I): 3.5
Reflection shellResolution: 2.29→2.32 Å / Num. unique obs: 5279 / CC1/2: 0.428

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→97.51 Å / SU ML: 0.3289 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.048
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2478 4219 4.89 %
Rwork0.224 82109 -
obs0.2252 86328 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.67 Å2
Refinement stepCycle: LAST / Resolution: 2.29→97.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7734 0 0 174 7908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00837919
X-RAY DIFFRACTIONf_angle_d0.86610716
X-RAY DIFFRACTIONf_chiral_restr0.0531168
X-RAY DIFFRACTIONf_plane_restr0.00761392
X-RAY DIFFRACTIONf_dihedral_angle_d18.13572924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.320.34921500.33432549X-RAY DIFFRACTION93.75
2.32-2.340.33411470.33242676X-RAY DIFFRACTION99.37
2.34-2.370.30051240.29992697X-RAY DIFFRACTION98.98
2.37-2.40.32791470.29492727X-RAY DIFFRACTION98.9
2.4-2.430.30881550.27762680X-RAY DIFFRACTION98.88
2.43-2.470.29971380.28222704X-RAY DIFFRACTION99.61
2.47-2.50.32671220.28142736X-RAY DIFFRACTION99.37
2.5-2.540.31191580.26082667X-RAY DIFFRACTION98.88
2.54-2.580.28921670.25252671X-RAY DIFFRACTION98.99
2.58-2.620.30781290.25732756X-RAY DIFFRACTION99.41
2.62-2.670.33891300.25662718X-RAY DIFFRACTION99.75
2.67-2.720.28511530.25252680X-RAY DIFFRACTION99.4
2.72-2.770.29551260.26272762X-RAY DIFFRACTION99.59
2.77-2.820.32251300.2542722X-RAY DIFFRACTION99.58
2.82-2.890.31431360.27512745X-RAY DIFFRACTION99.41
2.89-2.950.29251190.28012735X-RAY DIFFRACTION99.55
2.95-3.030.29681270.25892768X-RAY DIFFRACTION99.55
3.03-3.110.33841530.25382727X-RAY DIFFRACTION99.79
3.11-3.20.26321340.24092747X-RAY DIFFRACTION99.69
3.2-3.30.26951430.23592732X-RAY DIFFRACTION99.97
3.3-3.420.23981300.23182735X-RAY DIFFRACTION99.76
3.42-3.560.25591390.2212775X-RAY DIFFRACTION99.9
3.56-3.720.22881490.22132727X-RAY DIFFRACTION99.65
3.72-3.920.20281340.19622788X-RAY DIFFRACTION99.86
3.92-4.160.21231580.18522751X-RAY DIFFRACTION99.9
4.16-4.480.18511350.18362788X-RAY DIFFRACTION99.9
4.48-4.940.221390.17692780X-RAY DIFFRACTION99.97
4.94-5.650.21791460.20532802X-RAY DIFFRACTION99.73
5.65-7.120.22041690.2262807X-RAY DIFFRACTION99.87
7.12-97.510.17631320.16882957X-RAY DIFFRACTION99.39

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