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- PDB-5xvi: Crystal Structure of Aspergillus niger Apo- Glutamate Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 5xvi
TitleCrystal Structure of Aspergillus niger Apo- Glutamate Dehydrogenase
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / Aspergillus / Glutamate / Dehydrogenase / 2-oxoglutarate / Allostery
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 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate dehydrogenase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPrakash, P. / Punekar, N.S. / Bhaumik, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyRamalingaswami Re-entry Fellowship India
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for the catalytic mechanism and alpha-ketoglutarate cooperativity of glutamate dehydrogenase.
Authors: Prakash, P. / Punekar, N.S. / Bhaumik, P.
History
DepositionJun 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)296,8398
Polymers296,6556
Non-polymers1842
Water10,539585
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24890 Å2
ΔGint-14 kcal/mol
Surface area92190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.800, 92.820, 111.690
Angle α, β, γ (deg.)103.46, 94.17, 120.13
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glutamate dehydrogenase


Mass: 49442.508 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold)
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: B6V7E4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 3350, 0.1 M NaCl, 0.1 M Tris-Cl, pH 8.5, 0.01 M BaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 69072 / % possible obs: 92 % / Redundancy: 2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 6502 / CC1/2: 0.84 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SBO

3sbo


Resolution: 2.8→35 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.765 / SU B: 22.555 / SU ML: 0.428 / Cross valid method: THROUGHOUT / ESU R Free: 0.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31011 3451 5 %RANDOM
Rwork0.22571 ---
obs0.22987 65578 91.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.449 Å2
Baniso -1Baniso -2Baniso -3
1--3.46 Å2-1.4 Å20.94 Å2
2---2.29 Å21.43 Å2
3---5.06 Å2
Refinement stepCycle: 1 / Resolution: 2.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20813 0 12 585 21410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01921378
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220172
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.94128937
X-RAY DIFFRACTIONr_angle_other_deg2.083346397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87952790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52324.632965
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.868153493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.88215115
X-RAY DIFFRACTIONr_chiral_restr0.0750.23120
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0224999
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025024
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1562.77511050
X-RAY DIFFRACTIONr_mcbond_other1.1562.77511049
X-RAY DIFFRACTIONr_mcangle_it1.9814.1613815
X-RAY DIFFRACTIONr_mcangle_other1.9814.1613816
X-RAY DIFFRACTIONr_scbond_it0.8912.79510328
X-RAY DIFFRACTIONr_scbond_other0.8912.79510328
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5784.17515101
X-RAY DIFFRACTIONr_long_range_B_refined3.60821.5224212
X-RAY DIFFRACTIONr_long_range_B_other3.60421.5224211
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 237 -
Rwork0.31 4512 -
obs--86.41 %

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