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- PDB-6xeq: Crystal structure of the tetrameric 6-phosphogluconate dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 6xeq
TitleCrystal structure of the tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxidans
Components6-phosphogluconate dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / pentose phosphate pathway / tetramer
Function / homology
Function and homology information


phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) / D-gluconate metabolic process / phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt / NADP binding
Similarity search - Function
6-phosphogluconate dehydrogenase, YqeC-type / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
6-phosphogluconate dehydrogenase, NAD(+)-dependent, decarboxylating
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMaturana, P. / Roversi, P. / Castro-Fernandez, V. / Herrera-Morande, A. / Garratt, R.C. / Cabrera, R.
Funding support Chile, 1items
OrganizationGrant numberCountry
Comision Nacional Cientifica y Technologica (CONICYT)FONDEQUIP EQM140151 Chile
CitationJournal: Wellcome Open Res / Year: 2021
Title: Crystal structure of the 6-phosphogluconate dehydrogenase from Gluconobacter oxydans reveals tetrameric 6PGDHs as the crucial intermediate in the evolution of structure and cofactor preference ...Title: Crystal structure of the 6-phosphogluconate dehydrogenase from Gluconobacter oxydans reveals tetrameric 6PGDHs as the crucial intermediate in the evolution of structure and cofactor preference in the 6PGDH family [version 1; peer review: 1 approved, 1 approved with reservations]
Authors: Maturana, P. / Tobar-Calfucoy, E. / Fuentealba, M. / Roversi, P. / Garratt, R. / Cabrera, R.
History
DepositionJun 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase
B: 6-phosphogluconate dehydrogenase
C: 6-phosphogluconate dehydrogenase
D: 6-phosphogluconate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,7128
Polymers153,3284
Non-polymers3844
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25290 Å2
ΔGint-231 kcal/mol
Surface area49230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.061, 125.675, 166.273
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

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Components

#1: Protein
6-phosphogluconate dehydrogenase / 6PGDH


Mass: 38332.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Gene: GOX1705 / Production host: Escherichia coli (E. coli)
References: UniProt: G5EBD7, phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 2 M (NH4)2SO4 and 5% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45866 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45866 Å / Relative weight: 1
ReflectionResolution: 3.2→100.26 Å / Num. obs: 30273 / % possible obs: 98.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 46.51 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.092 / Rrim(I) all: 0.13 / Χ2: 0.5 / Net I/σ(I): 6.7
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3938 / CC1/2: 0.757 / Rpim(I) all: 0.327 / Rrim(I) all: 0.462 / Χ2: 0.53 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Cootmodel building
XDSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 4.0E+21 / Resolution: 3.2→100.26 Å / SU ML: 0.4297 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.758
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2859 1494 4.96 %
Rwork0.2457 28606 -
obs0.2477 30100 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.02 Å2
Refinement stepCycle: LAST / Resolution: 3.2→100.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9634 0 20 69 9723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029832
X-RAY DIFFRACTIONf_angle_d0.444713269
X-RAY DIFFRACTIONf_chiral_restr0.03951423
X-RAY DIFFRACTIONf_plane_restr0.00351755
X-RAY DIFFRACTIONf_dihedral_angle_d14.21065782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.30.39011130.36342220X-RAY DIFFRACTION84.84
3.3-3.420.35981180.31682546X-RAY DIFFRACTION96.45
3.42-3.560.29791620.27522585X-RAY DIFFRACTION99.57
3.56-3.720.30991290.26682618X-RAY DIFFRACTION99.6
3.72-3.920.30411450.24222632X-RAY DIFFRACTION99.75
3.92-4.160.30371270.23022638X-RAY DIFFRACTION99.39
4.16-4.480.23891540.21162614X-RAY DIFFRACTION99.82
4.48-4.930.24451310.21272670X-RAY DIFFRACTION99.86
4.93-5.650.22181350.21272675X-RAY DIFFRACTION99.79
5.65-7.120.3041330.24062693X-RAY DIFFRACTION99.61
7.12-100.27351470.22992715X-RAY DIFFRACTION95.53
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.034743129018-0.0160305723879-0.0519444217610.009396446601760.02771061648230.10399372730.0327224819487-0.014424658768-0.00723802156882-0.0274047442144-0.0150969356041-0.03866673725460.009193759014420.1175271882120.1408657791430.279630475240.0537244230531-0.01550606087760.5396872026650.2443820779620.31551017976638.2456102837-0.43598481083146.5844062523
20.1608376128640.04165813678020.01329246268460.01374707616360.009407052909330.01878253868750.09358133030230.0180481737726-0.173843085307-0.0983432929998-0.0437574568576-0.05815650722920.0317306557699-0.007451121988010.01197733398160.6293637493470.1706326871180.02248353888540.1854411992730.1108602740840.3108809655430.3876509485-5.3409680912532.7180008073
30.0531634545411-0.0243116272619-0.03039547804830.166333348216-0.05249483626030.063603534150.06353654062650.0171742624790.03794265639010.04515006282450.01857752355580.00861996219088-0.07738601472580.002534403294620.1352887709590.240818535914-0.0180711381617-0.05507111516240.1391052252470.1084374087960.25470916498823.38162560567.5286898077844.5474035284
40.175597568130.02848941473990.1303710405070.1301633015970.06665514057590.115926568596-0.056654024985-0.05975161615430.08676362300820.00172820092485-0.05567507137610.08834649842050.07094434674850.00963855199973-0.099627996350.360077621453-0.09591101166130.02519300608650.1504041276330.1109478701090.39887921610312.82494600038.8943966685942.0763947436
50.201206803029-0.1229223542580.0545620104030.0803272876834-0.07270028748960.3575165544270.0310369676984-0.1740627086670.024410242112-0.02365704872410.136323952159-0.003918571572910.1058207454050.1070377659220.1415182474820.2310663564920.08790456960330.03712057816070.2114379039830.01385413513760.24346726811428.107741679626.138568360530.3796999606
60.0417640443734-0.04848536941020.006331247688130.0539230861383-0.002752832241680.007547755733170.0666605550919-0.0222016872910.06302956881260.00441580213575-0.0204354728964-0.0685404491991-0.00463461062407-0.000606482917444-0.04395004674190.2860019145050.0009415864980190.08731775136950.327006464517-0.1199360465560.22966969461930.929907559142.77358214637.101576772
70.009766696005940.00345704018418-0.01095259276290.0077633607629-0.005092599575320.007548126835410.00613942167441-0.04823422451110.117637322175-0.0771194511111-0.0947333481994-0.1366069030920.002044533662910.09811147371790.0001546450643440.3682448760320.0715029854862-0.04744324719630.359536333885-0.0005327517489930.20872066843630.655739407922.753059322331.273332311
80.0211726708678-0.00491161118045-0.0298046353690.01040458434950.02517938392460.08083928118330.0272148328694-0.00740440626871-0.04309420225060.00543251715710.05023489127770.002370214965560.02487808269920.01193889798090.0622145066560.2001930385450.0944537645652-0.1060706679120.2772999539370.05633900551910.25919883554227.879343510723.790214177417.6395441128
90.00381274173397-0.001735528024370.00135677432260.00168222337256-0.002275462453990.002721862376650.001026786243070.01583354385570.04999881665080.00335953973657-0.0659834723716-0.03882903796810.01445023382840.0037759600783-2.48623017982E-60.6285241812610.0113230335575-0.2297980544990.8199325445740.07214495920210.48671239584737.881304248238.8556140944-0.861923322992
100.00746359491546-0.0208759985847-0.004658090354570.0725492829820.01229264071590.11617735662-0.07394132685170.00179975389996-0.0662459914745-0.0711260883162-0.0397951670306-0.004452757891250.0959299648542-0.119228190996-0.07030301168060.1674346451980.1423808211550.1061558889410.344149236944-0.2633478797590.1879270072867.04667809789.84627915552-18.8282963043
110.00425163972877-0.01708625264170.01335267094320.07569186531960.003550393963550.112749374196-0.0489933969093-0.1361134790540.003143751176380.0443171916720.0238486712571-0.002398272664660.133155862075-0.0619869024994-0.02081921291140.3090782558070.1166316797470.008454634939450.555660155369-0.07110327271610.12824943324813.73325570385.13594205564-6.46987582717
120.15305652928-0.01373571967170.04196313366480.03522266653290.04166064891950.08676756105650.0200424899532-0.0414772668542-0.03637559760890.02513364351120.01118545264410.07380134797820.0552293411587-0.0153369902674-0.003359287254110.3224532185930.164555991685-0.06257280084160.206063840597-0.04911315649320.21853284195421.517800348514.2642592099-11.6265982269
130.0139458011839-0.04748671536430.04414711660050.113427161803-0.1143668855410.11415905227-0.02036662727180.102929576414-0.003026911174880.09064253899440.122028658938-0.182273485495-0.0885569963614-0.07410515150540.0171739522260.1759896605340.1824708391380.04624201760720.421089112426-0.05711688702380.27567903773424.173963316528.0760064252-3.95155980111
140.00787426530741-0.01310662917240.01458240917060.0941270709252-0.04583352778140.0241400808647-0.01178058602480.0256118240005-0.01897707170150.04737931715260.07463879283620.14740004266-0.0956661837955-0.1051699079690.09612083295620.2997698433750.187750368289-0.04856144018890.2380817918230.1021823653050.25147288918213.607450855646.25072184870.214677267217
150.01653423486490.0178441717509-0.008634883908270.018427156691-0.006943169110260.004123376059550.05492017505210.0462254930032-0.07109526054070.02414736273130.08607981350650.1502992200080.033676694642-0.007925917770890.1154464744590.3129492252510.223821675736-0.07891759008690.3677522289090.01498276848350.26875038229716.370198275425.644763423319.576306345
160.198936135725-0.0339418515460.05415094784280.06058122158960.008452532950850.0209276504430.08575783305530.0922409121273-0.03334871658860.003739840087630.0753962248906-0.02100185336660.07168020956430.1100845057730.1129201341270.5422328721530.150242099525-0.1146047604780.6341570355770.2366093400160.37218735608830.698897880364.9679598131-13.0092267146
170.0677376203632-0.01901497638470.02984682981920.00647797305732-0.01079665115840.0182082884332-0.01898125602150.0365392803841-0.0324770096092-0.0135031617632-0.0665400253506-0.0725952437639-0.03719888076840.133972192193-0.09718454576170.4620298193860.0945183510563-0.144738707390.5222204029010.2592948742760.36167048397738.255761529466.7036820784-11.5639656059
180.08983194970020.0948897612974-0.01560665221330.11280930157-0.01034655316750.0311607551879-0.04620866780670.2095561269940.2854035230140.00224137655184-0.119428754551-0.00228010188605-0.1575706753260.0649013998276-0.1516003263350.4403083320770.234656738106-0.1535448742580.360269993590.1241306529580.36780377303626.608404390661.9471937792-2.22896969824
190.002382970570850.00905324182815-0.005366028475360.0412146402718-0.02458711750770.0147504209967-0.0294945201597-0.0192656366547-0.00836121894666-0.0214656666910.000247930575120.0469548781935-0.02420825398750.00304720370973-0.0414135222130.2197540827640.216670183707-0.1469627661360.5198249696110.1263719966050.36728766150912.372850736953.9176311966-8.23880211436
200.08062418929740.03534814940560.006156222247220.01731957732370.008644940787180.01474771923230.009978052205130.146955736717-0.09856458180470.05042079219730.047403115951-0.05664693775230.06793948698320.02550600386470.02730326901080.3421879017760.269953810642-0.09248259877540.260624216805-0.05324484136340.1462318973429.480904890728.79197651920.113416461203
210.03317393805290.032337601696-0.03078308702780.0314383910237-0.02997974643430.02888783208510.0912286248867-0.00604000689124-0.03221309088270.009787781038010.0897546019714-0.0133091961706-0.0309101565233-0.007954017059490.01154446395810.1895589274770.0895667071117-0.02415757004890.478285383331-0.1037357377170.24569463558633.945791248535.3465820311-6.29538627807
220.0763580179995-0.0125525896722-0.008539402715960.0328785154007-0.07173622913070.164069616240.0472821750349-0.0171720208502-0.1555609587930.1021243791250.126038217027-0.0805300395174-0.05333959399340.02915573186760.1233309524390.3637155275870.1987271327370.08630229387640.192184903145-0.01090635653460.32412586723225.329722809743.047793319214.5811629751
230.0005094363527490.0005194331158790.00143058959854-0.0001246816505790.0003871711627250.002201730302610.02137506705240.0337046759335-0.002271278211250.007667630693730.0124437991177-0.01499587787610.0560103710242-0.00145072705333-1.18803277102E-50.675572538370.201879767753-0.01401128373190.661824736636-0.06479709953990.45736316059538.203147723725.106738226332.9842562269
240.0288875420813-0.00364029512545-0.03049523159790.04109690203480.02214495170830.0414764775638-0.001102873350580.0813377101381-0.01017996220020.0746634438794-0.01752200122320.0959398320368-0.0563472828026-0.1699542231210.01511816402290.4306672097790.1178215041720.08840716061720.708223346045-0.1992245246590.3387422105549.0283387478949.748097776452.2574650591
250.1187393888320.01737723759020.0902515509210.03032549081360.0240078063030.08315721592320.106568555457-0.03728401138830.0522288868960.00884845271476-0.09396905714510.0397534286284-0.190518897754-0.2707061289460.03182503106740.4841411988840.1803180256770.05679182827570.379708476724-0.1744806180150.30499841090115.149130406152.894325167646.0576070956
260.401426553748-0.161431270854-0.2331505371130.2492049414160.1724134078910.3152610227740.0771712870558-0.2452920156620.05993711310640.01834715611670.104007371923-0.201358853870.06776230115440.03557597005020.2364186484840.3195157520250.111064870471-0.08658829835420.220522092623-0.0345355058680.16095586715524.189107103834.787337644837.6033943035
270.350061051343-0.0275525586297-0.09285978641050.005239788268580.006162273043030.02676550913390.0194544711844-0.232198326804-0.0258290346014-0.02129719513110.1074458716480.1291014471920.0646689112692-0.03048110671670.08010370723420.361249251068-0.0312209317001-0.02188139586150.2467664407180.1178390212460.202188709713.920936103616.851572006333.5199394056
280.03844514586260.0016411934171-0.02886264963480.197401083253-0.0633862642240.04267898048020.07797086608420.09429420352730.06407446955820.05100716286160.1605169600960.220760804299-0.02852946615110.006248263140360.03805013656750.3372560146640.1785199492470.01668724515290.3699752354080.01425766973640.26925609481716.994291610537.083856095814.5915185014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 168 )
4X-RAY DIFFRACTION4chain 'A' and (resid 169 through 191 )
5X-RAY DIFFRACTION5chain 'A' and (resid 192 through 222 )
6X-RAY DIFFRACTION6chain 'A' and (resid 223 through 251 )
7X-RAY DIFFRACTION7chain 'A' and (resid 252 through 289 )
8X-RAY DIFFRACTION8chain 'A' and (resid 290 through 309 )
9X-RAY DIFFRACTION9chain 'A' and (resid 310 through 327 )
10X-RAY DIFFRACTION10chain 'B' and (resid -2 through 67 )
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 103 )
12X-RAY DIFFRACTION12chain 'B' and (resid 104 through 168 )
13X-RAY DIFFRACTION13chain 'B' and (resid 169 through 222 )
14X-RAY DIFFRACTION14chain 'B' and (resid 223 through 277 )
15X-RAY DIFFRACTION15chain 'B' and (resid 278 through 326 )
16X-RAY DIFFRACTION16chain 'C' and (resid -4 through 11 )
17X-RAY DIFFRACTION17chain 'C' and (resid 12 through 67 )
18X-RAY DIFFRACTION18chain 'C' and (resid 68 through 168 )
19X-RAY DIFFRACTION19chain 'C' and (resid 169 through 191 )
20X-RAY DIFFRACTION20chain 'C' and (resid 192 through 251 )
21X-RAY DIFFRACTION21chain 'C' and (resid 252 through 278 )
22X-RAY DIFFRACTION22chain 'C' and (resid 279 through 307 )
23X-RAY DIFFRACTION23chain 'C' and (resid 308 through 326 )
24X-RAY DIFFRACTION24chain 'D' and (resid -2 through 32 )
25X-RAY DIFFRACTION25chain 'D' and (resid 33 through 168 )
26X-RAY DIFFRACTION26chain 'D' and (resid 169 through 222 )
27X-RAY DIFFRACTION27chain 'D' and (resid 223 through 279 )
28X-RAY DIFFRACTION28chain 'D' and (resid 280 through 324 )

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