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- PDB-8s3a: Crystal structure of Medicago truncatula glutamate dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 8s3a
TitleCrystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with 2,6-pyridinedicarboxylic acid and NAD
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / complex with inhibitor / glutamate dehydrogenase
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYRIDINE-2,6-DICARBOXYLIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glutamate dehydrogenase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGrzechowiak, M. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA 2018/31/D/NZ1/03630 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
D: Glutamate dehydrogenase
E: Glutamate dehydrogenase
F: Glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,79748
Polymers269,3646
Non-polymers6,43342
Water19,6721092
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34170 Å2
ΔGint-110 kcal/mol
Surface area82640 Å2
Unit cell
Length a, b, c (Å)84.794, 157.031, 94.882
Angle α, β, γ (deg.)90.000, 99.591, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glutamate dehydrogenase


Mass: 44894.016 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11433210, MTR_5g013470, MtrunA17_Chr5g0399821 / Production host: Medicago truncatula (barrel medic) / References: UniProt: G7JYL4

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Non-polymers , 9 types, 1134 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Na
#7: Chemical ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID


Mass: 167.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1092 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12 Ethylene glycols, 100mM imidazole/MES pH 6.5, 12.5% MPD, 12.5% PEG1000, 12.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.85→46.52 Å / Num. obs: 207412 / % possible obs: 99.8 % / Redundancy: 6.73 % / Biso Wilson estimate: 30.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.098 / Net I/σ(I): 11.36
Reflection shellResolution: 1.85→1.96 Å / Rmerge(I) obs: 1.013 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 33295 / CC1/2: 0.792 / Rrim(I) all: 1.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→46.52 Å / SU ML: 0.2123 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.199 1997 0.96 %
Rwork0.1567 205312 -
obs0.1571 207309 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.74 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18881 0 290 1092 20263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010619585
X-RAY DIFFRACTIONf_angle_d1.04226521
X-RAY DIFFRACTIONf_chiral_restr0.0582944
X-RAY DIFFRACTIONf_plane_restr0.00733449
X-RAY DIFFRACTIONf_dihedral_angle_d18.95757278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.32621400.27414448X-RAY DIFFRACTION98.52
1.9-1.950.26321430.247514578X-RAY DIFFRACTION99.85
1.95-2.010.28891420.22214683X-RAY DIFFRACTION99.95
2.01-2.070.27061410.214634X-RAY DIFFRACTION99.89
2.07-2.140.22851430.185114636X-RAY DIFFRACTION99.95
2.14-2.230.1991420.168314692X-RAY DIFFRACTION99.97
2.23-2.330.18531430.157814630X-RAY DIFFRACTION99.95
2.33-2.450.20491430.153214666X-RAY DIFFRACTION99.96
2.45-2.610.17811420.157114657X-RAY DIFFRACTION99.97
2.61-2.810.21151440.154814711X-RAY DIFFRACTION99.93
2.81-3.090.21481430.162914675X-RAY DIFFRACTION99.98
3.09-3.540.21651430.159714744X-RAY DIFFRACTION99.99
3.54-4.460.16631430.130814766X-RAY DIFFRACTION100
4.46-46.520.17431450.137514792X-RAY DIFFRACTION99.63
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)
12.131510777981.47093315812-0.3928828985851.91981227858-0.275306709991.40123027276-0.1291356939450.121043451024-0.248107435866-0.1348894190610.0565785088161-0.1418584534890.3697371182490.002157570908540.062519611010.2681578491620.008023267928860.01143122130150.255581478249-0.003368333608360.19612827083816.569160300956.888895905529.6162704438
21.342504790110.1484701311010.2986868733131.27631311179-0.5205432102331.200728306840.0575491604597-0.12049163469-0.303027394470.00850285813074-0.0969293746045-0.1925203312430.250745095025-0.01314134529780.03211141345480.281056006811-0.05928707869020.01536690013990.2575871534550.01689749802890.26150676828613.004807010843.267531096749.1906114079
31.50134414603-0.8904623385070.1469419608541.28953292808-0.4625687303311.72863693394-0.0221536250117-0.110923675480.179932508540.08036458801070.0457848323744-0.140391338216-0.3334099806480.102188107374-0.01934874693830.275651381302-0.04415944624150.004793684738180.289929244271-0.01142625193940.24387204409420.160578055196.913094273123.2446679737
41.74055695197-0.20773194604-0.6387436327831.708269942080.3487614605062.087595563270.156744436689-0.00812823045840.593999431693-0.3287637446930.17072653629-0.604121386261-0.9593327150040.615822254241-0.1286195367270.670802849601-0.2291468172780.1211872409980.502895252949-0.04721174594680.55055690390525.3608357064113.3843211766.12753389149
50.461245499587-0.140810771392-0.3609834807911.658845347890.582036730411.75610308909-0.01406716525660.0717251102735-0.00544911129853-0.101286804727-0.04496932658350.257368950506-0.0195552686864-0.5219840652960.0815284340420.211634388485-0.0752638164555-0.04329134788810.527098491743-0.003209866923520.286992222877-21.069419309171.472878468928.6916684545
61.173634552230.17426626645-0.1731477381431.08123121638-0.108568616720.737073878069-0.00517082399216-0.0792551710087-0.1730527697310.119612803652-0.006115585354450.3319037878060.1329286643-0.4233132642470.01232803712110.284439079813-0.1018024551060.004290715437950.564857153437-0.01437939026630.341762868236-29.298167530563.341704985949.6064625029
70.9401405169750.336582262824-0.2079331869791.56783993590.196439073551.5646101373-0.0221236519830.07652379017910.0464556295297-0.04606880158390.05611268177150.141568553184-0.0083680337648-0.4488281655860.00966357125320.2557234804160.0515713435288-0.03820175451560.4634442556120.02980312076240.277765153524-15.546366017389.529865925912.9114787345
81.625245503730.47320415604-1.190969026292.39875761551-1.569298847722.465337887070.05589487456260.830792781710.494200927816-0.430600910510.6716324577560.640709933516-0.181341098423-1.298441030620.0699395396460.3625271695520.153699092522-0.09372439998891.020876277230.3889764742330.437442265354-18.259234669997.2611086517-10.4792916931
91.777736785340.254351516516-0.5161884429120.5771513011080.02668808968711.50787803395-0.00192395963459-0.0361292336337-0.216341502583-0.0170062915218-0.0646574357081-0.04384681341120.3161399156160.008243125973980.06396813403430.319216923172-0.018976992807-0.008120857645640.262270048585-0.002302644562830.21926789210212.937386987562.13142992777.5263908363
100.720704178263-0.107492764977-1.19437685760.3995370615230.3037114914982.16761585052-0.04621374540130.0715591099031-0.00301655839213-0.04473719971850.01900039971030.009046928649440.181226259544-0.1824649324580.03465421502760.286565634743-0.0150350040407-0.01640893231940.3178807297150.004041782538330.24748480738812.499500536868.5283897849-13.5165657825
114.206856855070.184255146431.301177380781.77685302468-0.07043746907933.13878330038-0.0585715810720.194879210419-0.397097254646-0.141088708590.0942792434423-0.006863565586290.664060987167-0.227421867437-0.06034152144410.529093757894-0.07123762100050.05532619883160.318030306077-0.04974886626860.29301490521214.494224165952.9073543733-19.2268180569
123.14995562795-3.11669574424-2.765543905464.615286333182.928295574043.18728509363-0.171096709796-0.009668721511410.006119619087860.119686217130.116298805696-0.1195661198670.2848964071370.06459746403040.0499952972980.257602231115-0.0142516708177-0.02387919021040.267588477514-0.007481824618690.19814720268919.323934629368.0761730951-6.15191722805
134.22570837409-5.167648606212.073767190766.43052561186-2.148712086462.373885870240.009973331710890.3733846460670.743619301497-0.0910519212205-0.138191062367-0.393993493003-0.02814559604130.1971394557420.08439215373660.316748299708-0.01417792581740.009152923690550.339459938771-0.01592609750740.20008336966623.407907466477.7232220439-10.158784534
140.553716246613-0.004202302441741.653580099144.787861880954.256857319548.69684870033-0.0458658779187-0.06196115440840.00262248733467-0.1901390246920.02790691936050.0210911979479-0.1537610594770.264995144341-0.02453754328970.235983476174-0.009657838423310.01345858444270.3940284911140.02902063107560.2928326549431.330969450172.5780746864.71758209336
151.50384672956-0.5112073287160.1936416415510.887361400855-0.1760835421661.820236576640.03529440469660.01390927435620.1925112177470.0178107555916-0.0641096831099-0.0764870682563-0.2208595709230.1132141686570.03746547946170.25134760516-0.01918001551020.002827819815730.243054342867-0.01011546972630.22898140931810.558609301394.316003413945.1925686125
160.565570700761-0.173832189869-0.02996163288460.553919590097-0.04140417580521.52885674867-0.0169195926862-0.08824127396640.04368970041150.1226481771770.0249004053911-0.0284986875857-0.21838352386-0.0225315458379-0.008058362262590.277126684393-0.0142567585698-0.008641765313160.277336264066-0.0009772687934490.2412275741066.2089684318690.446107712462.1127982802
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 161 )AA2 - 1611 - 160
22chain 'A' and (resid 162 through 411 )AA162 - 411161 - 410
33chain 'B' and (resid 3 through 183 )BK3 - 1831 - 184
44chain 'B' and (resid 184 through 411 )BK184 - 411185 - 412
55chain 'C' and (resid 2 through 161 )CP2 - 1611 - 160
66chain 'C' and (resid 162 through 411 )CP162 - 411161 - 410
77chain 'D' and (resid 7 through 183 )DT7 - 1831 - 177
88chain 'D' and (resid 184 through 411 )DT184 - 411178 - 408
99chain 'E' and (resid 0 through 161 )EY0 - 1611 - 165
1010chain 'E' and (resid 162 through 228 )EY162 - 228166 - 232
1111chain 'E' and (resid 229 through 308 )EY229 - 308233 - 312
1212chain 'E' and (resid 309 through 358 )EY309 - 358313 - 362
1313chain 'E' and (resid 359 through 384 )EY359 - 384363 - 388
1414chain 'E' and (resid 385 through 411 )EY385 - 411389 - 415
1515chain 'F' and (resid -1 through 146 )FF-1 - 1461 - 154
1616chain 'F' and (resid 147 through 411 )FF147 - 411155 - 419

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