[English] 日本語
Yorodumi
- PDB-6vpb: A novel membrane-bound 6-phosphogluconate dehydrogenase from the ... -

+
Open data


ID or keywords:

Loading...

-
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 / organic acid catabolic process / pentose-phosphate shunt / NADP binding / metal ion 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more