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- PDB-10gw: Crystal structure of tetrameric 6-phosphogluconate dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 10gw
TitleCrystal structure of tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxydans in complex with 6-phosphogluconate
Components6-phosphogluconate dehydrogenase
KeywordsOXIDOREDUCTASE / Oxidative pentose phosphate pathway / 6-phosphogluconate dehydrogenase / dehydrogenase
Function / homology
Function and homology information


phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / D-gluconate metabolic process / 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-PHOSPHOGLUCONIC ACID / 6-phosphogluconate dehydrogenase, NAD(+)-dependent, decarboxylating
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMaturana, P. / Roversi, P. / Villalobos, P. / Gonzalez-Ordenes, F. / Castro-Fernandez, V. / Cabrera, R.
Funding support Chile, 1items
OrganizationGrant numberCountry
Comision Nacional Cientifica y Technologica (CONICYT)21141100 Chile
Citation
Journal: Arch.Biochem.Biophys. / Year: 2026
Title: Structural, dynamic, and evolutionary determinants of substrate binding in the tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxydans.
Authors: Maturana, P. / Villalobos, P. / Roversi, P. / Cabrera, R.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJan 19, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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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)154,4338
Polymers153,3284
Non-polymers1,1054
Water6,774376
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.118, 79.241, 86.533
Angle α, β, γ (deg.)102.168, 96.996, 99.404
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 and (name N or name...
d_2ens_1(chain "B" and ((resid 1 and (name N or name...
d_3ens_1(chain "C" and ((resid 1 and (name N or name...
d_4ens_1(chain "D" and ((resid 1 and (name N or name...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETASPASPAA1 - 3022 - 51
d_12THRTHRSERSERAA32 - 3353 - 54
d_13VALVALGLYGLYAA35 - 9156 - 112
d_14GLYGLYLEULEUAA93 - 133114 - 154
d_15GLYGLYTHRTHRAA136 - 144157 - 165
d_16GLUGLUPROPROAA146 - 153167 - 174
d_17LEULEUASPASPAA155 - 172176 - 193
d_18ALAALATHRTHRAA174 - 262195 - 283
d_19SERSERGLUGLUAA264 - 330285 - 351
d_1106PG6PG6PG6PGAE401
d_21METMETASPASPBB1 - 3022 - 51
d_22THRTHRSERSERBB32 - 3353 - 54
d_23VALVALGLYGLYBB35 - 9156 - 112
d_24GLYGLYLEULEUBB93 - 133114 - 154
d_25GLYGLYTHRTHRBB136 - 144157 - 165
d_26GLUGLUPROPROBB146 - 153167 - 174
d_27LEULEUASPASPBB155 - 172176 - 193
d_28ALAALATHRTHRBB174 - 262195 - 283
d_29SERSERGLUGLUBB264 - 330285 - 351
d_2106PG6PG6PG6PGBF401
d_31METMETASPASPCC1 - 3022 - 51
d_32THRTHRSERSERCC32 - 3353 - 54
d_33VALVALGLYGLYCC35 - 9156 - 112
d_34GLYGLYLEULEUCC93 - 133114 - 154
d_35GLYGLYTHRTHRCC136 - 144157 - 165
d_36GLUGLUPROPROCC146 - 153167 - 174
d_37LEULEUASPASPCC155 - 172176 - 193
d_38ALAALATHRTHRCC174 - 262195 - 283
d_39SERSERGLUGLUCC264 - 330285 - 351
d_3106PG6PG6PG6PGCG401
d_41METMETASPASPDD1 - 3022 - 51
d_42THRTHRSERSERDD32 - 3353 - 54
d_43VALVALGLYGLYDD35 - 9156 - 112
d_44GLYGLYLEULEUDD93 - 133114 - 154
d_45GLYGLYTHRTHRDD136 - 144157 - 165
d_46GLUGLUPROPRODD146 - 153167 - 174
d_47LEULEUASPASPDD155 - 172176 - 193
d_48ALAALATHRTHRDD174 - 262195 - 283
d_49SERSERGLUGLUDD264 - 330285 - 351
d_4106PG6PG6PG6PGDH401

NCS oper:
IDCodeMatrixVector
1given(-0.640340870406, 0.762743809032, -0.090473484905), (0.761144585271, 0.614326963455, -0.207993515007), (-0.103065464635, -0.202050151584, -0.973936982686)-1.37962056044, 5.84196326326, 40.8841048608
2given(0.53304194729, -0.650192996278, 0.541401283727), (-0.655245372136, -0.722053615845, -0.222018193264), (0.535275428844, -0.236405675559, -0.810920817244)-28.5786219776, -31.638259805, 43.0581995683
3given(-0.884899444361, -0.108267952343, -0.45302430825), (-0.111833639709, -0.894773998765, 0.432287783963), (-0.452157285024, 0.433194577101, 0.779677015161)-10.6987498804, -44.1361855547, 7.87864081825

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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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G5EBD7, phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating)
#2: Sugar
ChemComp-6PG / 6-PHOSPHOGLUCONIC ACID


Type: D-saccharide / Mass: 276.135 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS at pH 6.5 and 28% w/v polyethylene glycol monomethyl ether 2,000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2→41.61 Å / Num. obs: 90117 / % possible obs: 97.44 % / Redundancy: 3.5 % / Biso Wilson estimate: 35.31 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.06872 / Rpim(I) all: 0.0428 / Rrim(I) all: 0.08125 / Net I/σ(I): 9.56
Reflection shellResolution: 2→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 2909 / CC1/2: 0.629 / Rpim(I) all: 0.6375 / Rrim(I) all: 1.223 / % possible all: 96.19

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDS0.86data reduction
Aimless0.8.2data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→41.61 Å / SU ML: 0.2369 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.728
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 4536 5.04 %
Rwork0.1935 85515 -
obs0.1951 90051 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.31 Å2
Refinement stepCycle: LAST / Resolution: 2→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10096 0 68 376 10540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006510351
X-RAY DIFFRACTIONf_angle_d0.928213980
X-RAY DIFFRACTIONf_chiral_restr0.05291510
X-RAY DIFFRACTIONf_plane_restr0.00781852
X-RAY DIFFRACTIONf_dihedral_angle_d18.2453847
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.604049099001
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.676050518398
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.701066831486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.40061440.36812761X-RAY DIFFRACTION96.16
2.02-2.050.40591360.33872826X-RAY DIFFRACTION95.98
2.05-2.070.31311250.30692882X-RAY DIFFRACTION96.1
2.07-2.10.37881530.28662813X-RAY DIFFRACTION96.14
2.1-2.130.29141640.27962756X-RAY DIFFRACTION96.27
2.13-2.150.29531590.26512864X-RAY DIFFRACTION96.34
2.15-2.190.30661440.27322772X-RAY DIFFRACTION96.17
2.19-2.220.28241700.27152802X-RAY DIFFRACTION96.93
2.22-2.250.25791530.25082858X-RAY DIFFRACTION96.82
2.25-2.290.32011600.24182820X-RAY DIFFRACTION96.85
2.29-2.330.26751390.23072893X-RAY DIFFRACTION97.24
2.33-2.370.22391490.20092821X-RAY DIFFRACTION97.12
2.37-2.420.24211580.19152814X-RAY DIFFRACTION97.38
2.42-2.470.22611690.19272873X-RAY DIFFRACTION97.47
2.47-2.520.19961350.19452825X-RAY DIFFRACTION97.4
2.52-2.580.21051660.19422897X-RAY DIFFRACTION97.98
2.58-2.640.25271380.19732866X-RAY DIFFRACTION97.72
2.64-2.710.2541550.19712864X-RAY DIFFRACTION97.99
2.71-2.790.22391520.2062842X-RAY DIFFRACTION97.88
2.79-2.880.2511520.20372886X-RAY DIFFRACTION97.91
2.88-2.990.2291430.20042879X-RAY DIFFRACTION98.34
2.99-3.110.21731370.20332867X-RAY DIFFRACTION98.11
3.11-3.250.23421570.20442867X-RAY DIFFRACTION97.67
3.25-3.420.24731640.20342876X-RAY DIFFRACTION98.16
3.42-3.630.22241420.17432878X-RAY DIFFRACTION98.34
3.63-3.910.16341420.17122890X-RAY DIFFRACTION98.54
3.91-4.310.16851390.14362876X-RAY DIFFRACTION98.43
4.31-4.930.1771540.14612916X-RAY DIFFRACTION98.52
4.93-6.210.19561790.18272860X-RAY DIFFRACTION99.12
6.21-41.610.22321580.17682871X-RAY DIFFRACTION98.12
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)
11.258735666170.295251330180.4954920102091.917149855950.3193993280582.68530184069-0.1846685297790.4813196221510.26996580098-0.2693359635920.01922466533530.0363803807729-0.170925022401-0.2658367868120.1258645213710.446959000597-0.0233064871758-0.04324794565940.7994636821940.1601731991250.3470212661462.514428871411.31588205494-10.0004062183
21.977269261731.38138670822-1.147276274191.21039823982-0.9212438107641.33309975736-0.0288434751650.4831327357630.573140911502-0.04800434122870.2082173062930.31995649009-0.0421742098781-0.164469417497-0.08723670573130.2595163546090.0560397857039-0.05332849129770.4221419879280.1179863681570.406970196744-7.44689991955-4.00006244216.6297640317
31.304612030560.238660167788-0.3144372475831.58085796715-0.4730350075141.863254967040.654054134497-0.6685344246541.008122080721.12402193253-0.58902631426-0.103831526313-0.9244772601760.4875392171320.06804119943991.07897487399-0.428229317220.1798646985130.696326193637-0.3082347133990.921396645263-3.0584655185912.258065362646.1558637842
42.517616104770.766547971585-1.137045917921.18498807976-0.5151479228331.10686031045-0.0543147952854-0.149823702821-0.1241718553420.0267462278077-0.10164341432-0.1044400755020.06758956887340.2305228643120.1569238673990.2695528339360.0497540831824-0.04288053236450.3738239622630.05743138987170.2783352367811.35130262815-12.837412192923.9708871661
51.7539805041-1.16649458306-0.3790356585930.8406148466610.1299635636661.677087242270.300447426653-0.3582560743460.2637146274140.374683786293-0.6176102167321.711678210890.223852153253-1.0789398837-0.06329459164910.482321779397-0.1189281687490.1012031439951.10770291549-0.3174768346411.36642853042-41.7352312036-35.861301539550.2932346671
62.198913459241.37664358727-0.1833261466873.423479171060.6965010110282.177364774440.211833420328-0.982954647341-0.5424077984820.41057896616-0.7589141758930.1030282222540.272551130065-0.08390084639070.3647166847540.394206021193-0.05221091305020.06457840691680.7148516207470.1338958947270.472886661712-25.7883262851-34.315949245850.9744747113
73.007590974410.904646468189-1.586911070371.48872665798-0.6920566618591.10428095797-0.3341903853570.622399565488-0.00744193258308-0.2112623275240.2516507426050.2094398131480.206382112966-0.4496323938430.0770501610820.324981638047-0.0514129390328-0.05609861640460.4959003564830.03354568251890.299341070783-21.3105280042-22.410601950520.3771724051
80.6261177448910.672050909262-0.1340309839521.06812713693-0.1010758866210.230872569631-0.8069645858070.779332477722-1.81255876865-0.7072593646320.159439945061-1.026928245890.7542712302190.281695291406-0.8646949025141.36364991808-0.2885094173280.8756662655061.08556776159-0.84397524321.71078326866-8.35726261948-49.8462488449-0.629406779559
92.888703616670.982773027311-1.609539394141.5770913145-0.6023591910491.56484956271-0.596635352580.208820879587-0.963718617194-0.3684832292760.085823445266-0.3244234948930.470364163576-0.09191931881740.0143760812090.3911087409260.02641465357260.1121047251250.27103626274-0.02430096081760.461802801806-11.3149823957-32.566817617422.4783320734
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 144 )AA-2 - 1441 - 147
22chain 'A' and (resid 145 through 332 )AA145 - 332148 - 335
33chain 'B' and (resid -2 through 191 )BD-2 - 1911 - 194
44chain 'B' and (resid 192 through 331 )BD192 - 331195 - 334
55chain 'C' and (resid 1 through 53 )CG1 - 531 - 53
66chain 'C' and (resid 54 through 191 )CG54 - 19154 - 191
77chain 'C' and (resid 192 through 331 )CG192 - 331192 - 331
88chain 'D' and (resid 0 through 144 )DJ0 - 1441 - 145
99chain 'D' and (resid 145 through 331 )DJ145 - 331146 - 332

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