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- PDB-5xw0: Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Co... -

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Basic information

Entry
Database: PDB / ID: 5xw0
TitleCrystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Isophthalate and NADPH
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / Aspergillus / Glutamate / Dehydrogenase / Isophthalate / Inhibition / NADPH / Coenzyme / Reaction mechanism
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
benzene-1,3-dicarboxylic acid / Chem-NDP / DI(HYDROXYETHYL)ETHER / Glutamate dehydrogenase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)51,97620
Polymers49,4431
Non-polymers2,53319
Water5,531307
1
A: Glutamate dehydrogenase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)311,855120
Polymers296,6556
Non-polymers15,200114
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 area59980 Å2
ΔGint-12 kcal/mol
Surface area77430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.480, 173.480, 241.140
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-827-

HOH

21A-895-

HOH

31A-900-

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, 326 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-8G0 / benzene-1,3-dicarboxylic acid


Mass: 166.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 7.06 Å3/Da / Density % sol: 82.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES (pH 6.0) 30% (v/v) PEG 200, 5 % (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: 1.9→70 Å / Num. obs: 109208 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 15446 / CC1/2: 0.61 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.719 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18038 5460 5 %RANDOM
Rwork0.16805 ---
obs0.16867 103738 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.006 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å2-0 Å2
2--0.17 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 166 307 3946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193747
X-RAY DIFFRACTIONr_bond_other_d0.0070.023532
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9795057
X-RAY DIFFRACTIONr_angle_other_deg0.9538142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8025477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78524.691162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75615590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2121519
X-RAY DIFFRACTIONr_chiral_restr0.0860.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024251
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02853
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_it1.6632.8511855
X-RAY DIFFRACTIONr_mcbond_other1.6612.8511854
X-RAY DIFFRACTIONr_mcangle_it2.44.2682321
X-RAY DIFFRACTIONr_mcangle_other2.4014.2682322
X-RAY DIFFRACTIONr_scbond_it2.4223.1881892
X-RAY DIFFRACTIONr_scbond_other2.4063.1891892
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8354.642727
X-RAY DIFFRACTIONr_long_range_B_refined5.93923.8944401
X-RAY DIFFRACTIONr_long_range_B_other5.6623.4844295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 402 -
Rwork0.297 7635 -
obs--99.64 %

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