[English] 日本語
Yorodumi
- PDB-7ymu: Structure of Alcohol dehydrogenase from [Candida] glabrata -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ymu
TitleStructure of Alcohol dehydrogenase from [Candida] glabrata
ComponentsNADPH-dependent methylglyoxal reductase GRE2
KeywordsOXIDOREDUCTASE / oxidoreducatse
Function / homology
Function and homology information


steroid biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
3-beta hydroxysteroid dehydrogenase/isomerase / 3-beta hydroxysteroid dehydrogenase/isomerase family / : / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / NADPH-dependent methylglyoxal reductase GRE2
Similarity search - Component
Biological species[Candida] glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)2207821 China
CitationJournal: To Be Published
Title: Rationla design of CgADH from candida glarata for asymmetric reduction of azacycolne.
Authors: Sun, Z.W. / Liu, Y.F. / Xu, G.C. / Ni, Y.
History
DepositionJul 29, 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
B: NADPH-dependent methylglyoxal reductase GRE2
C: NADPH-dependent methylglyoxal reductase GRE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,11527
Polymers117,1873
Non-polymers1,92824
Water15,475859
1
A: NADPH-dependent methylglyoxal reductase GRE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,75310
Polymers39,0621
Non-polymers6919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH-dependent methylglyoxal reductase GRE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5237
Polymers39,0621
Non-polymers4616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NADPH-dependent methylglyoxal reductase GRE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,83910
Polymers39,0621
Non-polymers7779
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.570, 102.750, 179.690
Angle α, β, γ (deg.)90.000, 95.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-812-

HOH

21A-821-

HOH

-
Components

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


Mass: 39062.262 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Candida] glabrata (fungus) / Gene: AO440_001055, AO440_004721 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W0CJZ6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 859 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 1.2M Ammonium citrate tribasic, 8% PEG 2000, pH 7.3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.987 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jan 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→46.62 Å / Num. obs: 97729 / % possible obs: 98.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 29.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Net I/σ(I): 13.4 / Num. measured all: 655074 / Scaling rejects: 109
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.935.40.7142249141650.7980.3330.7922.184.6
10.41-46.626.20.05338486190.9960.0230.05831.897.5

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6K

5b6k


Resolution: 1.9→44.71 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 4863 4.98 %
Rwork0.1875 92823 -
obs0.1899 97686 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.73 Å2 / Biso mean: 34.3599 Å2 / Biso min: 14.72 Å2
Refinement stepCycle: final / Resolution: 1.9→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8070 0 126 859 9055
Biso mean--46.33 40.66 -
Num. residues----1026
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.920.32571260.30072569269583
1.92-1.940.34331610.29392750291188
1.94-1.970.30871440.27562907305194
1.97-1.990.30871610.263231463307100
1.99-2.020.31861860.246330433229100
2.02-2.050.31261480.245531913339100
2.05-2.080.32961620.231931273289100
2.08-2.110.30931590.227130983257100
2.11-2.140.25331770.22431513328100
2.14-2.170.28581760.21830793255100
2.17-2.210.26431730.215631203293100
2.21-2.250.28371710.226230833254100
2.25-2.30.26871580.212431623320100
2.3-2.340.29221590.204130793238100
2.34-2.390.28941780.207731933371100
2.39-2.450.26351710.205830563227100
2.45-2.510.24041520.204631573309100
2.51-2.580.25681690.207331643333100
2.58-2.650.27571590.201230583217100
2.65-2.740.25351610.202331253286100
2.74-2.840.27191480.202231993347100
2.84-2.950.25711650.201831443309100
2.95-3.090.25491790.194331033282100
3.09-3.250.22511740.186931223296100
3.25-3.450.23531360.17831963332100
3.45-3.720.21241450.1631093254100
3.72-4.090.18621620.150831823344100
4.09-4.680.17231750.141731303305100
4.68-5.90.18191650.164131733338100
5.9-44.710.20981630.16513207337099

+
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