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- PDB-7ecr: Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 7ecr
TitleCrystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Succinate and ADP-ribose
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / Glutamate dehydrogenase / allostery / Aspergillus / enzyme 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 domain superfamily
Similarity search - Domain/homology
Chem-A2R / SUCCINIC ACID / Glutamate dehydrogenase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsGodsora, B.K.J. / Prakash, P. / Punekar, N.S. / Bhaumik, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Proteins / Year: 2022
Title: Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites.
Authors: Godsora, B.K.J. / Prakash, P. / Punekar, N.S. / Bhaumik, P.
History
DepositionMar 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate dehydrogenase
B: Glutamate dehydrogenase
C: Glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,85629
Polymers147,7423
Non-polymers4,11426
Water26,5901476
1
A: Glutamate dehydrogenase
B: Glutamate dehydrogenase
C: Glutamate dehydrogenase
hetero molecules

A: Glutamate dehydrogenase
B: Glutamate dehydrogenase
C: Glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,71358
Polymers295,4856
Non-polymers8,22852
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area39190 Å2
ΔGint-8 kcal/mol
Surface area80280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.880, 153.750, 259.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11C-639-

HOH

21C-1104-

HOH

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Components

#1: Protein Glutamate dehydrogenase /


Mass: 49247.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Succinate and ADP-ribose / Source: (gene. exp.) Aspergillus terreus (mold) / Gene: gdhA, ATETN484_0007063400 / Production host: Escherichia coli (E. coli) / References: UniProt: T2D1F5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A2R / [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE


Mass: 639.296 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H24N5O17P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1476 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.06 Å3/Da / Density % sol: 69.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.8 M Succinic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→38.68 Å / Num. obs: 246054 / % possible obs: 99.2 % / Redundancy: 7.11 % / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.11 / Net I/σ(I): 15.38
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 5.93 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 36141 / CC1/2: 0.72 / Rrim(I) all: 0.1 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XVX

5xvx


Resolution: 1.73→38.68 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.649 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.167 12303 5 %RANDOM
Rwork0.145 ---
obs0.14616 233751 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.827 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å2-0 Å20 Å2
2--0.1 Å2-0 Å2
3---1.25 Å2
Refinement stepCycle: 1 / Resolution: 1.73→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10401 0 264 1476 12141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.01911054
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210163
X-RAY DIFFRACTIONr_angle_refined_deg2.121.96914992
X-RAY DIFFRACTIONr_angle_other_deg1.101323610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92851439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53124.426479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.162151773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6031563
X-RAY DIFFRACTIONr_chiral_restr0.1370.21639
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212499
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022273
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_it1.7561.7845590
X-RAY DIFFRACTIONr_mcbond_other1.7551.7845589
X-RAY DIFFRACTIONr_mcangle_it2.1822.6647002
X-RAY DIFFRACTIONr_mcangle_other2.1822.6647003
X-RAY DIFFRACTIONr_scbond_it3.0342.0255463
X-RAY DIFFRACTIONr_scbond_other3.0292.0255463
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2852.9367961
X-RAY DIFFRACTIONr_long_range_B_refined5.23922.82313270
X-RAY DIFFRACTIONr_long_range_B_other5.23922.82713271
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.733→1.778 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 868 -
Rwork0.332 16498 -
obs--95.69 %

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