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- PDB-5xvx: Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Co... -

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Basic information

Entry
Database: PDB / ID: 5xvx
TitleCrystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Alpha-ketoglutarate and NADPH
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / Aspergillus / Glutamate / Dehydrogenase / 2-Oxoglutarate / Allostery / NADPH / Coenzyme / Reaction mechanism
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 / Chem-NDP / DI(HYDROXYETHYL)ETHER / Glutamate dehydrogenase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,66428
Polymers49,4431
Non-polymers3,22227
Water12,142674
1
A: Glutamate dehydrogenase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)315,987168
Polymers296,6556
Non-polymers19,332162
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area69710 Å2
ΔGint-13 kcal/mol
Surface area77850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.460, 174.460, 240.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-935-

HOH

21A-1044-

HOH

31A-1154-

HOH

41A-1203-

HOH

51A-1217-

HOH

61A-1238-

HOH

71A-1270-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate dehydrogenase /


Mass: 49442.508 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 701 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 674 / 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: 7.12 Å3/Da / Density % sol: 82.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium citrate (pH 5.5), 20% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / Num. obs: 128967 / % possible obs: 99.6 % / Redundancy: 12.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.092 / Net I/σ(I): 17.08
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 18853 / CC1/2: 0.96 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.171 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14799 6448 5 %RANDOM
Rwork0.13518 ---
obs0.13582 122517 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.177 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.11 Å2-0 Å2
2--0.21 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.8→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 210 674 4357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193961
X-RAY DIFFRACTIONr_bond_other_d0.0060.023768
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9825368
X-RAY DIFFRACTIONr_angle_other_deg0.97938708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.985523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89924.602176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93115638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91523
X-RAY DIFFRACTIONr_chiral_restr0.1010.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024541
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02917
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_it1.6672.4631924
X-RAY DIFFRACTIONr_mcbond_other1.6612.4631923
X-RAY DIFFRACTIONr_mcangle_it2.2333.6892428
X-RAY DIFFRACTIONr_mcangle_other2.2353.6892429
X-RAY DIFFRACTIONr_scbond_it2.6612.9462037
X-RAY DIFFRACTIONr_scbond_other2.6542.9472037
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9324.2172914
X-RAY DIFFRACTIONr_long_range_B_refined9.04523.8545177
X-RAY DIFFRACTIONr_long_range_B_other7.67321.3634676
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 455 -
Rwork0.268 8640 -
obs--95.85 %

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