[English] 日本語
Yorodumi
- PDB-7ymb: Structure of Alcohol dehydrogenase from Candida glabrata(CgADH)co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ymb
TitleStructure of Alcohol dehydrogenase from Candida glabrata(CgADH)complexed with NADPH
ComponentsNADPH-dependent methylglyoxal reductase GRE2
KeywordsOXIDOREDUCTASE / ketoreducatse
Function / homology3-beta hydroxysteroid dehydrogenase/isomerase / 3-beta hydroxysteroid dehydrogenase/isomerase family / : / steroid biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD(P)-binding domain superfamily / nucleotide binding / Chem-NDP / NADPH-dependent methylglyoxal reductase GRE2
Function and homology information
Biological species[Candida] glabrata (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSun, Z.W. / Liu, Y.F. / Xu, G.C. / Ni, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22078127 China
CitationJournal: To Be Published
Title: rational desigen of CgADH from Candida glabrata for stereocomplementary reduction of azacyclone.
Authors: Sun, Z.W. / Ni, Y. / Xu, G.C.
History
DepositionJul 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADPH-dependent methylglyoxal reductase GRE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8082
Polymers39,0621
Non-polymers7451
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-4 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.644, 48.322, 70.475
Angle α, β, γ (deg.)90.000, 96.630, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein NADPH-dependent methylglyoxal reductase GRE2 / Alcohol dehydrogenase


Mass: 39062.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Candida] glabrata (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W0CJZ6
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium acetate, 0.1M sodium acetate pH 4.6, 30% PEG 4000

-
Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jul 29, 2021 / Details: multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.739→24.59 Å / Num. obs: 32695 / % possible obs: 95.05 % / Redundancy: 2.93 % / Rsym value: 0.156 / Net I/av σ(I): 66.672 / Net I/σ(I): 10.3
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.289 / Num. unique obs: 1678

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6K

5b6k


Resolution: 1.8→24.59 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 1489 4.91 %RANDOM
Rwork0.1855 28845 --
obs0.1872 30334 95.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.8 Å2 / Biso mean: 21.0281 Å2 / Biso min: 6.45 Å2
Refinement stepCycle: final / Resolution: 1.8→24.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 48 298 3038
Biso mean--14.96 28.27 -
Num. residues----343
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.860.32421440.2542549269394
1.86-1.920.28511360.23472544268095
1.92-20.25041620.21582580274296
2-2.090.2391270.20222590271796
2.09-2.20.21961370.19652654279196
2.2-2.340.23741300.19232604273496
2.34-2.520.25921150.19192678279397
2.52-2.770.21111220.18932626274897
2.78-3.180.22011490.18422639278896
3.18-40.19351420.1672636277896
4-24.590.18031250.15962745287097

+
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