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- PDB-5xvv: Crystal Structure of Forward Inhibited Aspergillus niger Glutamat... -

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Basic information

Entry
Database: PDB / ID: 5xvv
TitleCrystal Structure of Forward Inhibited Aspergillus niger Glutamate Dehydrogenase With Both Apo- and Alpha Ketoglutarate Bound Subunits
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / Aspergillus / Glutamate / Dehydrogenase / 2-Oxoglutarate / Allostery / Forward Inhibition / 2-Mercaptoethanol
Function / homology
Function and homology information


glutamate dehydrogenase (NADP+) activity / amino acid metabolic process / nucleotide binding
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / BETA-MERCAPTOETHANOL / Glutamate dehydrogenase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 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

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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)299,58837
Polymers296,6556
Non-polymers2,93331
Water27,3111516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32920 Å2
ΔGint-13 kcal/mol
Surface area89250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.260, 92.150, 111.060
Angle α, β, γ (deg.)103.40, 93.95, 120.36
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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1516 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.15 M potassium bromide, 20% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→35 Å / Num. obs: 135737 / % possible obs: 95.5 % / Redundancy: 2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.96
Reflection shellResolution: 2.25→2.35 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 15991 / CC1/2: 0.68 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→33 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.523 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19863 6786 5 %RANDOM
Rwork0.15826 ---
obs0.16029 128936 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.927 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.29 Å2-0.37 Å2
2---0.11 Å20.1 Å2
3---0.61 Å2
Refinement stepCycle: 1 / Resolution: 2.25→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20806 0 186 1516 22508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01921517
X-RAY DIFFRACTIONr_bond_other_d0.0070.0220324
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.94629070
X-RAY DIFFRACTIONr_angle_other_deg0.971346737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22852787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36924.643967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.635153486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.75415115
X-RAY DIFFRACTIONr_chiral_restr0.0840.23139
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0225039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025028
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_it1.3552.42511043
X-RAY DIFFRACTIONr_mcbond_other1.3552.42511042
X-RAY DIFFRACTIONr_mcangle_it2.2033.63213808
X-RAY DIFFRACTIONr_mcangle_other2.2033.63213809
X-RAY DIFFRACTIONr_scbond_it2.0362.69410474
X-RAY DIFFRACTIONr_scbond_other2.0362.69410474
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1983.92915244
X-RAY DIFFRACTIONr_long_range_B_refined5.96119.86525483
X-RAY DIFFRACTIONr_long_range_B_other5.95319.84425411
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 477 -
Rwork0.24 9050 -
obs--90.98 %

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