[English] 日本語
Yorodumi
- PDB-6kwt: Crystal structure of Gre2 in complex with NADPH complex from Cand... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kwt
TitleCrystal structure of Gre2 in complex with NADPH complex from Candida albicans
ComponentsMethylglyoxal reductase (NADPH-dependent)
KeywordsOXIDOREDUCTASE / Gre2 / methylglyoxal reductase / NADPH
Function / homology3-beta hydroxysteroid dehydrogenase/isomerase family / : / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / nucleotide binding / Chem-NDP / Methylglyoxal reductase (NADPH-dependent)
Function and homology information
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsNguyen, G.T. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2019R1A2C4069796 Korea, Republic Of
CitationJournal: Crystals / Year: 2019
Title: Crystal Structure of NADPH-Dependent Methylglyoxal Reductase Gre2 from Candida Albicans
Authors: Nguyen, G.T. / Kim, S. / Jin, H. / Cho, D.H. / Chun, H.S. / Kim, W.K. / Chang, J.H.
History
DepositionSep 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methylglyoxal reductase (NADPH-dependent)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0612
Polymers37,3161
Non-polymers7451
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-6 kcal/mol
Surface area15100 Å2
Unit cell
Length a, b, c (Å)152.447, 152.447, 152.447
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

-
Components

#1: Protein Methylglyoxal reductase (NADPH-dependent)


Mass: 37316.074 Da / Num. of mol.: 1 / Fragment: 295 / Mutation: Q52K, 295Edeletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / Gene: orf19.5611, CAALFM_C603240WA / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ABT9
#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
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium citrate tribasic dihydrate (pH5.6), 20% v/v 2-propanol, 20% w/v polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.02→50 Å / Num. obs: 11745 / % possible obs: 100 % / Redundancy: 41.1 % / CC1/2: 0.999 / Net I/σ(I): 32
Reflection shellResolution: 3.02→3.07 Å / Num. unique obs: 592 / CC1/2: 0.815

-
Processing

Software
NameVersionClassification
PHENIX1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2108 1403 -
Rwork0.1724 --
obs0.1762 11745 100 %
Refinement stepCycle: LAST / Resolution: 3.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 48 0 2684

+
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