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- PDB-8s38: Crystal structure of Medicago truncatula glutamate dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 8s38
TitleCrystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with citrate and NAD
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / glutamic acid / NAD cofactor / nitrogen metabolism
Function / homology
Function and homology information


glutamate dehydrogenase (NAD+) activity / L-glutamate catabolic process / nucleotide binding / mitochondrion / metal ion 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
CITRIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glutamate dehydrogenase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsGrzechowiak, M. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre Poland
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Legume-type glutamate dehydrogenase: Structure, activity, and inhibition studies.
Authors: Grzechowiak, M. / Sliwiak, J. / Link, A. / Ruszkowski, M.
History
DepositionFeb 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,77847
Polymers134,6823
Non-polymers4,09644
Water14,862825
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15820 Å2
ΔGint48 kcal/mol
Surface area46540 Å2
Unit cell
Length a, b, c (Å)95.368, 163.100, 219.023
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11B-509-

NA

21A-830-

HOH

31B-793-

HOH

41B-801-

HOH

51B-808-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Glutamate dehydrogenase


Mass: 44894.016 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11433210, MTR_5g013470, MtrunA17_Chr5g0399821 / Production host: Escherichia coli (E. coli) / References: UniProt: G7JYL4

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Non-polymers , 8 types, 869 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.18 Å3/Da / Density % sol: 61.33 % / Description: rod
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM MgCl2 , 100 mM Na-citrate pH 5.0, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 292 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.89→99 Å / Num. obs: 135999 / % possible obs: 99.9 % / Redundancy: 6.74 % / Biso Wilson estimate: 34.74 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.067 / Net I/σ(I): 18.29
Reflection shellResolution: 1.89→2 Å / Redundancy: 6.73 % / Rmerge(I) obs: 0.899 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 21745 / CC1/2: 0.73 / Rrim(I) all: 0.974 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→59.64 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 1360 1 %1360
Rwork0.1579 134639 --
obs0.1582 135999 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.15 Å2
Refinement stepCycle: LAST / Resolution: 1.89→59.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9405 0 262 825 10492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01059928
X-RAY DIFFRACTIONf_angle_d1.029113404
X-RAY DIFFRACTIONf_chiral_restr0.06031477
X-RAY DIFFRACTIONf_plane_restr0.00721750
X-RAY DIFFRACTIONf_dihedral_angle_d16.92153677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.960.30061360.261313263X-RAY DIFFRACTION98.95
1.96-2.040.23331350.215113354X-RAY DIFFRACTION99.91
2.04-2.130.22131350.19313358X-RAY DIFFRACTION99.99
2.13-2.240.21541350.174713362X-RAY DIFFRACTION99.93
2.24-2.380.19291350.158213407X-RAY DIFFRACTION99.86
2.38-2.560.19181360.157813419X-RAY DIFFRACTION99.94
2.56-2.820.19711360.15813478X-RAY DIFFRACTION99.99
2.82-3.230.16861360.155813499X-RAY DIFFRACTION99.98
3.23-4.070.17441380.141213574X-RAY DIFFRACTION100
4.07-59.640.17721400.1513925X-RAY DIFFRACTION99.69
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.49550497114-0.6781066888460.3839935570271.95724962101-0.2785975872950.579406542026-0.011789535221-0.1592873854680.009701406456810.186026738537-0.05217060538520.003499969190230.00396125460192-0.04275067984770.06341596630140.253102646604-0.003165076305490.02815201244160.265866585295-0.009278302680910.23063854066537.4833327094114.661215287166.135108736
21.546564250190.490123638263-0.1795724092051.15523879077-0.3942964253711.240909769090.0637799677001-0.307200300982-0.1396425788270.264430972657-0.03769186088980.240017012495-0.0173117103665-0.211583925822-0.02940519494820.3216691846960.02051371569710.06701831974780.2757952469050.004615621593930.31963488601427.978199092993.4085436683173.288794932
31.836249296020.086845930227-1.130654406160.607996176091-0.04509503885251.523688509710.08330035356380.2001234666580.037091576695-0.125288121798-0.06790881741270.114349756961-0.0631860236294-0.182260189706-0.0377021676690.2705887455420.0669312915249-0.05976572555350.26777763813-0.02562038891870.25284025666127.5522816247119.738936357129.70742437
42.12687288074-0.09605107400220.2704944291891.173669905470.4788231470671.6861854548-0.001283276191510.474922552578-0.262147369537-0.15474038067-0.07353973269940.1486192355630.197763885816-0.2503103565030.06486114290910.276649850839-0.02471864233630.01163174052190.329096913447-0.0450314753910.26968890491710.2455131811103.601211766128.112118452
50.566304042650.1153080125190.5833952320830.9317911460360.104663659251.62270130341-0.003824309077730.117568971129-0.00879022116463-0.174858744288-0.086895240753-0.1374041206160.1187946266950.2216299730790.06617665496490.2854933373330.08234109383690.03611972714520.2836281487430.04063135076810.31184498608160.9887273012101.968761796138.651996895
60.751420551071-0.3138012064250.2222951209791.93039929985-0.9105788073440.8512788890320.1078063833810.0502804732936-0.264901489957-0.453831211606-0.325250387699-0.3472902448860.5012940530110.3895582040230.1456804693830.53329951460.1345469109980.07747182743440.4341876102970.0696751294010.45478774508158.219010922782.3678196063134.287885492
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 183 )AA5 - 1831 - 188
22chain 'A' and (resid 184 through 411 )AA184 - 411189 - 419
33chain 'B' and (resid -2 through 183 )BL-2 - 1831 - 187
44chain 'B' and (resid 184 through 411 )BL184 - 411188 - 424
55chain 'C' and (resid -1 through 183 )CU-1 - 1831 - 191
66chain 'C' and (resid 184 through 411 )CU184 - 411192 - 425

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