[English] 日本語
Yorodumi
- PDB-7w5l: The crystal structure of the oxidized form of Gluconobacter oxyda... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w5l
TitleThe crystal structure of the oxidized form of Gluconobacter oxydans WSH-004 SNDH
ComponentsL-sorbosone dehydrogenase, NAD(P) dependent
KeywordsOXIDOREDUCTASE / L-sorbosone dehydrogenase / NAD(P)+
Function / homologyAldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, D. / Hou, X.D. / Rao, Y.J. / Zhou, J.W. / Chen, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31830068 China
CitationJournal: Adv Sci / Year: 2023
Title: Structural Insight into the Catalytic Mechanisms of an L-Sorbosone Dehydrogenase.
Authors: Li, D. / Deng, Z. / Hou, X. / Qin, Z. / Wang, X. / Yin, D. / Chen, Y. / Rao, Y. / Chen, J. / Zhou, J.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-sorbosone dehydrogenase, NAD(P) dependent


Theoretical massNumber of molelcules
Total (without water)54,4541
Polymers54,4541
Non-polymers00
Water2,594144
1
A: L-sorbosone dehydrogenase, NAD(P) dependent

A: L-sorbosone dehydrogenase, NAD(P) dependent

A: L-sorbosone dehydrogenase, NAD(P) dependent

A: L-sorbosone dehydrogenase, NAD(P) dependent


Theoretical massNumber of molelcules
Total (without water)217,8164
Polymers217,8164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_554y,x,-z-1/31
crystal symmetry operation10_444-y-1,-x-1,-z-1/31
Buried area15690 Å2
ΔGint-52 kcal/mol
Surface area63000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.018, 181.018, 77.593
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-626-

HOH

21A-703-

HOH

31A-734-

HOH

-
Components

#1: Protein L-sorbosone dehydrogenase, NAD(P) dependent


Mass: 54454.000 Da / Num. of mol.: 1 / Mutation: C296A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Strain: WSH-004 / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-TRIS pH 5.5, 2.0 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26284 / % possible obs: 100 % / Redundancy: 37.8 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.017 / Rrim(I) all: 0.109 / Χ2: 1.094 / Net I/σ(I): 6 / Num. measured all: 993880
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5937.61.21525640.9130.1981.2321.154100
2.59-2.6938.20.88625630.9560.1430.8981.123100
2.69-2.8237.70.63425690.9770.1030.6421.121100
2.82-2.9635.90.45326040.9860.0760.4591.135100
2.96-3.1537.80.29425850.9940.0480.2981.145100
3.15-3.3939.60.18326260.9980.0290.1851.161100
3.39-3.7339.30.10526130.9990.0170.1061.177100
3.73-4.2738.10.06726430.9990.0110.0681.148100
4.27-5.3839.10.047267610.0070.0481.028100
5.38-50350.034284110.0060.0340.7599.7

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U4J

3u4j


Resolution: 2.5→29.07 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 1230 4.71 %
Rwork0.1938 24858 -
obs0.1957 26088 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.74 Å2 / Biso mean: 40.4562 Å2 / Biso min: 16.5 Å2
Refinement stepCycle: final / Resolution: 2.5→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 0 144 3608
Biso mean---40.97 -
Num. residues----457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.60.29541460.25192677282399
2.6-2.720.28611410.232327082849100
2.72-2.870.30581250.220627542879100
2.87-3.040.26141230.227527402863100
3.05-3.280.2411310.208227682899100
3.28-3.610.25111420.187127522894100
3.61-4.130.20861290.170627992928100
4.13-5.20.21451470.15912800294799
5.2-29.070.19691460.19772860300696

+
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