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

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Basic information

Entry
Database: PDB / ID: 5xwc
TitleCrystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Alpha-iminoglutarate, 2-amino-2-hydroxyglutarate and NADP
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / Glutamate Dehydrogenase / Aspergillus niger / Alpha-iminoglutarate / 2-amino-2-hydroxyglutarate / NADP / Coenzyme / Reaction Intermediate
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
(2Z)-2-iminopentanedioic acid / (2S)-2-azanyl-2-oxidanyl-pentanedioic acid / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / Glutamate dehydrogenase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 29, 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)55,11354
Polymers49,4431
Non-polymers5,67053
Water9,494527
1
A: Glutamate dehydrogenase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)330,677324
Polymers296,6556
Non-polymers34,022318
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 area32420 Å2
ΔGint-27 kcal/mol
Surface area82540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.410, 173.410, 241.830
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-607-

HOH

21A-1080-

HOH

31A-1081-

HOH

41A-1104-

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 , 6 types, 580 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-8GL / (2S)-2-azanyl-2-oxidanyl-pentanedioic acid


Mass: 163.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO5
#4: Chemical ChemComp-2IT / (2Z)-2-iminopentanedioic acid


Mass: 145.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7NO4
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsThe author states that in this structure, the alpha-imino group of alpha-iminoglutarate is ...The author states that in this structure, the alpha-imino group of alpha-iminoglutarate is protonated. As this ligand is the reaction intermediate and the alpha-imino group forms an ionic interaction with the negatively charged carboxylate group of an active site asparate, it is highly possible that this group of the ligand is in the protonated form. The existing ligand (2IT) represents the neutral alpha-amino group, therefore does not satisfy the correct ionization state of the ligand present in this structure.

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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

Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40% v/v PEG 300, 0.1M sodium cacodylate, pH 6.5, 0.2 M calcium acetate hydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→35 Å / Num. obs: 138857 / % possible obs: 99 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.4
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.69 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→34 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.431 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16921 6920 5 %RANDOM
Rwork0.15545 ---
obs0.15613 131488 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.291 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.75→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 370 527 4366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193941
X-RAY DIFFRACTIONr_bond_other_d0.0080.023747
X-RAY DIFFRACTIONr_angle_refined_deg1.6542.0095267
X-RAY DIFFRACTIONr_angle_other_deg0.99238632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45924.545165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97615592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2181521
X-RAY DIFFRACTIONr_chiral_restr0.2010.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024315
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02875
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_it1.3662.2821869
X-RAY DIFFRACTIONr_mcbond_other1.3622.2821868
X-RAY DIFFRACTIONr_mcangle_it1.9563.4182345
X-RAY DIFFRACTIONr_mcangle_other1.9573.4182346
X-RAY DIFFRACTIONr_scbond_it2.6282.982072
X-RAY DIFFRACTIONr_scbond_other2.6282.982072
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9284.1852916
X-RAY DIFFRACTIONr_long_range_B_refined7.92321.9924814
X-RAY DIFFRACTIONr_long_range_B_other7.22720.4494535
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 511 -
Rwork0.371 9705 -
obs--99.89 %

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