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- PDB-6vpb: A novel membrane-bound 6-phosphogluconate dehydrogenase from the ... -

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Basic information

Entry
Database: PDB / ID: 6vpb
TitleA novel membrane-bound 6-phosphogluconate dehydrogenase from the acetic acid bacteria Gluconacetobacter diazotrophicus (Gd6PGD)
Components6-phosphogluconate dehydrogenase
KeywordsOXIDOREDUCTASE / 6-phosphogluconate dehydrogenase / Gluconacetobacter diazotrophicus / membrane-bound protein / 6-phospho-D-gluconate / NAD+
Function / homology
Function and homology information


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
ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / 6-phosphogluconate dehydrogenase
Similarity search - Component
Biological speciesGluconacetobacter diazotrophicus (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.87 Å
AuthorsRodriguez-Romero, A. / Rodriguez-Hernandez, A.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)299048 Mexico
CitationJournal: Febs J. / Year: 2021
Title: The structure of a novel membrane-associated 6-phosphogluconate dehydrogenase from Gluconacetobacter diazotrophicus (Gd6PGD) reveals a subfamily of short-chain 6PGDs.
Authors: Sarmiento-Pavia, P.D. / Rodriguez-Hernandez, A. / Rodriguez-Romero, A. / Sosa-Torres, M.E.
History
DepositionFeb 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 6-phosphogluconate dehydrogenase
B: 6-phosphogluconate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9705
Polymers71,7792
Non-polymers1913
Water6,287349
1
A: 6-phosphogluconate dehydrogenase
B: 6-phosphogluconate dehydrogenase
hetero molecules

A: 6-phosphogluconate dehydrogenase
B: 6-phosphogluconate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,94010
Polymers143,5594
Non-polymers3816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area25750 Å2
ΔGint-215 kcal/mol
Surface area43140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.760, 82.097, 81.831
Angle α, β, γ (deg.)90.000, 103.407, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

21A-668-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHR(chain 'A' and (resid 1 through 43 or (resid 44...AA1 - 1251 - 125
12LEULEUVALVAL(chain 'A' and (resid 1 through 43 or (resid 44...AA132 - 247132 - 247
13SERSERSERSER(chain 'A' and (resid 1 through 43 or (resid 44...AA250 - 276250 - 276
14GLYGLYTHRTHR(chain 'A' and (resid 1 through 43 or (resid 44...AA279 - 282279 - 282
15ALAALAPROPRO(chain 'A' and (resid 1 through 43 or (resid 44...AA285 - 294285 - 294
16THRTHRGLYGLY(chain 'A' and (resid 1 through 43 or (resid 44...AA297 - 323297 - 323
21METMETTHRTHR(chain 'B' and (resid 1 through 10 or (resid 11...BB1 - 1251 - 125
22LEULEUVALVAL(chain 'B' and (resid 1 through 10 or (resid 11...BB132 - 247132 - 247
23SERSERSERSER(chain 'B' and (resid 1 through 10 or (resid 11...BB250 - 276250 - 276
24GLYGLYTHRTHR(chain 'B' and (resid 1 through 10 or (resid 11...BB279 - 282279 - 282
25ALAALAPROPRO(chain 'B' and (resid 1 through 10 or (resid 11...BB285 - 294285 - 294
26THRTHRGLYGLY(chain 'B' and (resid 1 through 10 or (resid 11...BB297 - 323297 - 323

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Components

#1: Protein 6-phosphogluconate dehydrogenase / / 6-phosphogluconate dehydrogenase / decarboxylating


Mass: 35889.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / PAl5) (bacteria)
Strain: ATCC 49037 / DSM 5601 / PAl5 / References: UniProt: A9H324
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10 mM sodium phosphate pH 6.0, 0.1 % triton X-100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.87→36.48 Å / Num. obs: 48489 / % possible obs: 99.2 % / Redundancy: 16.5 % / Biso Wilson estimate: 25.68 Å2 / CC1/2: 0.953 / Rpim(I) all: 0.023 / Rrim(I) all: 0.097 / Net I/σ(I): 51.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→36.48 Å / SU ML: 0.2344 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0225
RfactorNum. reflection% reflection
Rfree0.2222 997 2.06 %
Rwork0.183 --
obs0.1838 48489 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.13 Å2
Refinement stepCycle: LAST / Resolution: 1.87→36.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 0 12 349 5093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00934859
X-RAY DIFFRACTIONf_angle_d1.00746592
X-RAY DIFFRACTIONf_chiral_restr0.0623738
X-RAY DIFFRACTIONf_plane_restr0.0072867
X-RAY DIFFRACTIONf_dihedral_angle_d7.56243891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.970.33781400.27746706X-RAY DIFFRACTION99.16
1.97-2.090.23971430.2176803X-RAY DIFFRACTION100
2.09-2.250.26661410.21366811X-RAY DIFFRACTION99.89
2.25-2.480.2531410.20746786X-RAY DIFFRACTION99.04
2.48-2.840.23831430.20276717X-RAY DIFFRACTION98.41
2.84-3.570.23521440.17766765X-RAY DIFFRACTION98.73
3.57-36.480.17031450.14596904X-RAY DIFFRACTION99.44

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