[English] 日本語
Yorodumi
- PDB-6pex: An aldo keto reductase with 2-keto- L-gulonate reductase activity -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pex
TitleAn aldo keto reductase with 2-keto- L-gulonate reductase activity
Componentsaldo keto reductase
KeywordsOXIDOREDUCTASE / D-isomer-specific 2-hydroxyacid dehydrogenase / L-tartaric acid pathway / 2-keto-L-gulonic acid / Ascorbic acid degradation
Function / homology
Function and homology information


glyoxylate reductase / glyoxylate reductase (NADH) activity / D-lactate dehydrogenase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / D-lactate dehydrogenase activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / NAD binding / cytosol
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glyoxylate/hydroxypyruvate/pyruvate reductase 2KGR
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.581 Å
AuthorsYong, J. / Crystal, S. / Robert, D.H. / John, B.B.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: An aldo-keto reductase with 2-keto-l-gulonate reductase activity functions in l-tartaric acid biosynthesis from vitamin C inVitis vinifera.
Authors: Jia, Y. / Burbidge, C.A. / Sweetman, C. / Schutz, E. / Soole, K. / Jenkins, C. / Hancock, R.D. / Bruning, J.B. / Ford, C.M.
History
DepositionJun 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: aldo keto reductase
B: aldo keto reductase
C: aldo keto reductase
D: aldo keto reductase


Theoretical massNumber of molelcules
Total (without water)144,5864
Polymers144,5864
Non-polymers00
Water19,4021077
1
A: aldo keto reductase


Theoretical massNumber of molelcules
Total (without water)36,1471
Polymers36,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: aldo keto reductase


Theoretical massNumber of molelcules
Total (without water)36,1471
Polymers36,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: aldo keto reductase


Theoretical massNumber of molelcules
Total (without water)36,1471
Polymers36,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: aldo keto reductase


Theoretical massNumber of molelcules
Total (without water)36,1471
Polymers36,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.050, 85.720, 112.900
Angle α, β, γ (deg.)90.000, 89.910, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
aldo keto reductase


Mass: 36146.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: VIT_09s0002g04300, VITISV_025327 / Organ: Berry / Production host: Escherichia coli (E. coli) / References: UniProt: A5CAL1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1077 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.26 M ammonium sulfate, 100 mM sodium acetate/acetic acid (pH 4.5), 200 mM sodium chloride.

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.58→47.15 Å / Num. obs: 188965 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.064 / Rrim(I) all: 0.121 / Net I/σ(I): 5.6 / Num. measured all: 661190 / Scaling rejects: 99
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 3 % / Rmerge(I) obs: 0.352 / Num. unique obs: 9119 / CC1/2: 0.919 / Rpim(I) all: 0.237 / Rrim(I) all: 0.427 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BAZ

3baz


Resolution: 1.581→27.7 Å / Cross valid method: THROUGHOUT / σ(F): 1.61 / Phase error: 33.62 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2513 9350 4.95 %
Rwork0.2299 179517 -
obs0.2498 188947 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.47 Å2 / Biso mean: 20.9948 Å2 / Biso min: 1.92 Å2
Refinement stepCycle: final / Resolution: 1.581→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9511 0 0 1077 10588
Biso mean---23.33 -
Num. residues----1248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5812-1.60840.45914480.43238734918293
1.6084-1.63770.43514300.40398993942395
1.6377-1.66920.41784560.37759000945695
1.6692-1.70320.38924680.3639004947295
1.7032-1.74020.38164840.35158989947395
1.7402-1.78070.30854560.3268931938795
1.7807-1.82520.34114810.3139012949395
1.8252-1.87450.31164570.30858991944895
1.8745-1.92960.30755130.29598917943094
1.9296-1.99180.28354250.27899067949295
1.9918-2.0630.27444670.26528940940795
2.063-2.14550.30044910.25439003949495
2.1455-2.2430.25384790.25479009948895
2.243-2.36110.29174770.2579007948495
2.3611-2.50870.30264390.25179022946195
2.5087-2.7020.27584330.24759046947995
2.702-2.97310.23475170.2278946946394
2.9731-3.40140.22444660.21029005947194
3.4014-4.27830.21584900.19338997948794
4.2783-19.83380.19064480.17718904935292

+
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://pdbjlvh1.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