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- PDB-6yeh: Arabidopsis thaliana glutamate dehydrogenase isoform 1 in apo form -

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Basic information

Entry
Database: PDB / ID: 6yeh
TitleArabidopsis thaliana glutamate dehydrogenase isoform 1 in apo form
ComponentsGlutamate dehydrogenase 1
KeywordsOXIDOREDUCTASE / glutamate dehydrogenase / 2-oxoglutarate / NAD / amino acid metabolism
Function / homology
Function and homology information


response to absence of light / glutamate dehydrogenase [NAD(P)+] activity / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / amino acid metabolic process / cobalt ion binding / plastid / copper ion binding / mitochondrion ...response to absence of light / glutamate dehydrogenase [NAD(P)+] activity / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / amino acid metabolic process / cobalt ion binding / plastid / copper ion binding / mitochondrion / zinc ion binding / ATP binding
Similarity search - Function
Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / 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 / Leucine Dehydrogenase, chain A, domain 1 / 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
: / Glutamate dehydrogenase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsRuszkowski, M. / Grzechowiak, M. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA 2018/31/D/NZ1/03630 Poland
CitationJournal: Front Plant Sci / Year: 2020
Title: Structural Studies of Glutamate Dehydrogenase (Isoform 1) FromArabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism.
Authors: Grzechowiak, M. / Sliwiak, J. / Jaskolski, M. / Ruszkowski, M.
History
DepositionMar 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate dehydrogenase 1
B: Glutamate dehydrogenase 1
C: Glutamate dehydrogenase 1
D: Glutamate dehydrogenase 1
E: Glutamate dehydrogenase 1
F: Glutamate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,66023
Polymers269,1256
Non-polymers1,53517
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23270 Å2
ΔGint-189 kcal/mol
Surface area87770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.570, 99.169, 318.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 4 - 411 / Label seq-ID: 7 - 414

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 4 through 411)AA
22(chain 'B' and resid 4 through 411)BB
33(chain 'C' and resid 4 through 411)CC
44(chain 'D' and resid 4 through 411)DD
55(chain 'E' and resid 4 through 411)EE
66(chain 'F' and resid 4 through 411)FF

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Components

#1: Protein
Glutamate dehydrogenase 1 / GDH 1


Mass: 44854.219 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GDH1, At5g18170, MRG7.13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)
References: UniProt: Q43314, glutamate dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% w/v PEG 4000, 100 mM Tris-HCl pH 7.5, 33% (v/v) MPD

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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: 0.8266 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 2.59→90 Å / Num. obs: 69315 / % possible obs: 88.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 44.03 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.074 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
2.59-2.768.51.072.334050.5810.3942.2
7.95-88.96.30.04326.434670.9980.02599.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AtGDH1-NAD

Resolution: 2.59→89.77 Å / SU ML: 0.3092 / Cross valid method: FREE R-VALUE / Phase error: 25.0225
Details: Hydrogen atoms at riding positions were added during refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 1044 1.51 %random
Rwork0.1827 ---
obs0.1835 69315 74.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.26 Å2
Refinement stepCycle: LAST / Resolution: 2.59→89.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18704 0 94 139 18937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006419153
X-RAY DIFFRACTIONf_angle_d0.849125911
X-RAY DIFFRACTIONf_chiral_restr0.05212892
X-RAY DIFFRACTIONf_plane_restr0.00553358
X-RAY DIFFRACTIONf_dihedral_angle_d19.26177067
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)
11.283608105430.284011141392-0.2873409761810.544541199281-0.2661423153181.639827907340.02895667073180.09167369415890.2163861923180.08558867618240.02292790608180.130876989724-0.17535977628-0.0408394323589-0.02991164047590.2240423584150.0319751347320.02779126294530.183593161284-0.01961260555560.39618751824812.044746996614.171683858138.115770267
25.00923339347-1.43225903278-0.3204276132464.781992501681.629999808413.473257394450.0276852448785-0.2631621143580.152010711979-0.024211000713-0.1937859000090.178304332787-0.197961297179-0.1758088210890.145896381190.312389809513-0.02482611144220.08561037344030.240789240192-0.04276846691810.236777087388-2.8898635596317.8551429863160.291857319
33.012045154251.14616263247-0.1539666808891.996940947661.108707600393.543922589480.156625733623-0.300064761137-0.2278618481760.211050665051-0.0832805069009-0.1697614483560.104589468491-0.072141958789-0.08627381331190.2181726646950.02247620840710.004779749452980.1042063334730.01614448995180.26192221805115.39328701652.53165525218151.045506116
41.232274910120.05982320003890.1097874255433.89576393656-1.636344374555.13407401167-0.100298088041-0.321534450571.068349608340.07603103158650.0368171495514-0.119237991754-1.13933346388-0.555084818710.01128018853990.5239573719590.09625971279160.04929627118810.3368542675520.004200209305990.86650874028418.050137251937.0031366031116.096991306
51.45856054384-1.056544215711.78021215552.08542998822-2.060214462615.06557886421-0.100758720697-0.04427518467230.4071574970820.19136796039-0.0153569681798-0.0759622862359-0.4817492895770.2496789634910.1275944494750.217792035544-0.01157512050310.04110265265040.203133983634-0.05806568999340.4114227705731.554014429424.2677023891125.538797552
62.73410929624-1.253879028711.449223922872.16914002539-1.278467022065.160415810850.101273690988-0.2095615605370.2377558350320.0658592073727-0.08670937575070.04561271015830.01381336980170.2947988596370.008144570170850.165668538022-0.004896422267260.02793335511910.146324410488-0.03873937627470.35020674974937.701716161418.0631533739126.738903005
73.73527684992-0.3479807919621.116001959033.66691133071-0.8032315966285.025066157470.00321840915391-0.134428694570.383407598826-0.02354258792360.114238361610.363319749960.332105085580.311446593728-0.1146263393680.2110303666110.009540905670410.04670789890290.15154765505-0.06616115216180.27820370149537.689296546514.3637130053120.462285223
82.39875024081.11147995923-1.168227495848.07371903375-1.962063858882.158722220750.0956153768290.133408759120.0652588308715-0.2893885488120.0746811604443-0.505223994194-0.1555770132830.160785845729-0.08588707981960.283028228252-0.04504381081690.07492032895280.346617758475-0.0775117239340.29315677681242.483263483125.741157597106.12281796
94.145015597221.239806121470.7651250452234.31707799422-0.3073752316552.774637628980.222075014408-0.01509740655140.734931334769-0.1537449492020.0685519692966-0.673702757421-0.7023096952420.877164801038-0.2499231047570.527645240386-0.1340080310620.2240828002010.530719171633-0.15660963770.87678460853752.956495390942.3682104468105.532630917
103.337014186880.635694337231-0.737098500183.426236516931.384484134663.093504293910.403951620117-0.7560238252820.629587906590.6170246654080.251726100509-0.639556932154-0.607741532891.61504929084-0.5584801023610.67153801002-0.2762986749930.09096157516970.756217270291-0.3592511993161.1274307526657.357598135244.062590144112.226077508
111.53535624769-0.809579129090.4069712035593.028239102352.112696748592.248512215780.242020333563-0.2203627659450.766821730240.61737235343-0.000335554736163-0.555685693001-0.6885016652480.356404986017-0.3078278777240.855579667117-0.1673971915760.2209918940290.41697350371-0.1586891695970.91648921959441.034538087351.0957483877113.129815629
122.413361449040.7593647605740.337217723216.979723634160.2527433684131.62513930377-0.044950128383-0.1820329109370.6644037421950.05137673134870.3728937161390.126138099588-0.5104182425730.0365961081837-0.2489426784440.3484736837630.001866598205260.09485287087420.265976899957-0.01715149818190.41863822023836.570817382533.4482473508108.096071439
137.93995911681-4.56505116382-0.2280141282223.48889949140.3182982267512.711578075810.9706653840410.7419677002760.385603800734-1.60736506775-0.2877362461160.603700926976-0.408681809189-0.341676939312-0.5409348619290.55807551750.01476176269810.0648180572560.4191901704370.1502197819150.61903512711333.503270060432.037939522597.9657964727
142.829228064320.919618674922-0.2768037442666.462694967550.9684445375743.750497246660.1149479053430.335883075131.166302427080.01170718748750.2752167800151.41643375522-0.344116906062-0.0366131684564-0.4536334757760.3482632177090.1125816174910.01347335608430.2614896670790.1038017313630.62846420291319.350755967133.0690391251107.514403916
151.832844070871.66370521694-0.2632363283262.507275652460.351992720241.79344520728-0.01460048978290.0164195346455-0.3526094498480.06472270234150.119342884843-0.323904041980.301561383140.321326644507-0.08381859568580.2819414280530.115521509044-0.09590911324550.247541604134-0.0607358893240.30854065082137.5449148917-16.1303626952132.065753902
161.37932274187-0.01851374787560.5653004262152.95755603873-0.07090873917831.684160950210.117718695622-0.261123078664-0.5200486263470.783919642306-0.0296285654029-0.4569766784740.5551300981670.325137601015-0.04904881588720.6254187587550.0888306753803-0.1251777347030.3494343342690.07349988266170.57137988687431.5757835978-28.512926513149.212846936
171.774962076070.929994099257-0.1984433634262.501767619330.09268246067711.678294929750.03331368233730.217648171693-0.317793647704-0.09377740928240.123309723319-0.3120156599120.33679635270.238970731476-0.1385572292820.2787499884510.104347129414-0.03279002919530.28379428243-0.1132882281740.31645321922143.3721722616-13.0454013676110.078078847
181.60318885448-0.561505837935-0.9667429517311.555095512720.7384940817735.571561810470.001329381579360.370066052892-0.0299239531935-0.4153929834170.177993552312-0.4479762109420.8801543750181.07051394184-0.1423152809270.628913044220.2150624681020.05343348734810.535670831106-0.1289190292580.44334912324657.236919802-5.3605352878592.7034065794
192.1066283688-0.43797061752-0.9514524813012.189038877170.7158184574321.89183101240.03068618626220.364958085115-0.128200501802-0.3448743659070.01536949131470.5002850450070.192127004185-0.344887087813-0.05000974909130.322561849059-0.0965295555456-0.1599879594070.378170878476-0.00898777704410.4610853863912.18630436732-14.379567602112.569303258
201.82838823959-1.053752161210.5110697851583.06557141355-1.778639032072.81797674970.274364926555-0.224473875464-0.954968737888-0.4908796363950.6251705785071.650706907741.01020383599-0.927355530196-0.2521381146260.571584584133-0.391253518574-0.3914855056830.5328451037230.21946887051.30038281966-11.9022555579-24.7525907336128.366341019
211.82855045825-0.673660184993-0.8548003367572.265636549580.5173799949622.327974211510.1020446278790.521420134124-0.0439750755875-0.387443228978-0.05646581681110.5031909391270.0699926111041-0.454358494506-0.005671795767670.308759605179-0.0181264945669-0.1676195885820.4847505498910.0746742318830.4156461942037.902603388072.2632526680798.060407934
221.86285737290.5338530219040.6260566189133.114204171180.0371699494482.97714049638-0.2684021544090.926023551530.445474189873-1.273772087880.3109797475920.848631766611-0.305417900682-0.287084623566-0.01357035831110.767367067396-0.134690816095-0.2889028992910.84360798750.2376796168940.62610869082914.636942540410.287680235877.7445623154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 200 )
2X-RAY DIFFRACTION2chain 'A' and (resid 201 through 338 )
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 411 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 32 )
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 94 )
6X-RAY DIFFRACTION6chain 'B' and (resid 95 through 131 )
7X-RAY DIFFRACTION7chain 'B' and (resid 132 through 161 )
8X-RAY DIFFRACTION8chain 'B' and (resid 162 through 200 )
9X-RAY DIFFRACTION9chain 'B' and (resid 201 through 249 )
10X-RAY DIFFRACTION10chain 'B' and (resid 250 through 287 )
11X-RAY DIFFRACTION11chain 'B' and (resid 288 through 308 )
12X-RAY DIFFRACTION12chain 'B' and (resid 309 through 358 )
13X-RAY DIFFRACTION13chain 'B' and (resid 359 through 384 )
14X-RAY DIFFRACTION14chain 'B' and (resid 385 through 411 )
15X-RAY DIFFRACTION15chain 'C' and (resid 4 through 161 )
16X-RAY DIFFRACTION16chain 'C' and (resid 162 through 411 )
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 161 )
18X-RAY DIFFRACTION18chain 'D' and (resid 162 through 411 )
19X-RAY DIFFRACTION19chain 'E' and (resid 2 through 161 )
20X-RAY DIFFRACTION20chain 'E' and (resid 162 through 411 )
21X-RAY DIFFRACTION21chain 'F' and (resid 4 through 161 )
22X-RAY DIFFRACTION22chain 'F' and (resid 162 through 411 )

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