[English] 日本語
Yorodumi
- PDB-8yai: Crystal structure of glucose 1-dehydrogenase mutant1 from Limosil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yai
TitleCrystal structure of glucose 1-dehydrogenase mutant1 from Limosilactobacillus fermentum
ComponentsSDR family oxidoreductase
KeywordsHYDROLASE / glucose 1-dehydrogenase
Function / homologyPKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / SDR family oxidoreductase
Function and homology information
Biological speciesLimosilactobacillus fermentum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsCong, L. / Wang, J.J. / Wei, H.L. / Liu, W.D. / You, S.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council China
CitationJournal: Adv.Synth.Catal. / Year: 2024
Title: Structure-Guided Engineering of a Short-Chain Dehydrogenase LfSDR1 for Efficient Biosynthesis of (R)-9-(2-Hydroxypropyl)adenine, the Key Intermediate of Tenofovir
Authors: Wang, Q. / Cong, L. / Guo, J. / Wang, J. / Han, X. / Zhang, W. / Liu, W. / Wei, H. / You, S.
History
DepositionFeb 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SDR family oxidoreductase
B: SDR family oxidoreductase
D: SDR family oxidoreductase
C: SDR family oxidoreductase


Theoretical massNumber of molelcules
Total (without water)105,2844
Polymers105,2844
Non-polymers00
Water6,107339
1
A: SDR family oxidoreductase
B: SDR family oxidoreductase
D: SDR family oxidoreductase

C: SDR family oxidoreductase


Theoretical massNumber of molelcules
Total (without water)105,2844
Polymers105,2844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y+1/2,-z1
Buried area12380 Å2
ΔGint-88 kcal/mol
Surface area30820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.205, 104.514, 72.331
Angle α, β, γ (deg.)90.000, 110.960, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 188 or resid 206 through 247))
21chain B
31(chain C and (resid 2 through 188 or resid 206 through 247))
41(chain D and (resid 2 through 188 or resid 206 through 247))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYALAALA(chain A and (resid 2 through 188 or resid 206 through 247))AA2 - 1882 - 188
12LYSLYSGLNGLN(chain A and (resid 2 through 188 or resid 206 through 247))AA206 - 247206 - 247
21GLYGLYGLNGLNchain BBB2 - 2472 - 247
31GLYGLYALAALA(chain C and (resid 2 through 188 or resid 206 through 247))CD2 - 1882 - 188
32LYSLYSGLNGLN(chain C and (resid 2 through 188 or resid 206 through 247))CD206 - 247206 - 247
41GLYGLYALAALA(chain D and (resid 2 through 188 or resid 206 through 247))DC2 - 1882 - 188
42LYSLYSGLNGLN(chain D and (resid 2 through 188 or resid 206 through 247))DC206 - 247206 - 247

-
Components

#1: Protein
SDR family oxidoreductase


Mass: 26321.000 Da / Num. of mol.: 4 / Mutation: G92V/E141L/G146D/V186A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus fermentum (bacteria)
Gene: GC247_10055 / Plasmid: pET-32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A843R2C6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.06 % / Mosaicity: 1.7 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1M Na Citrate pH 5.6, 0.15M NH4Ac, 29% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2022
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→30 Å / Num. obs: 45668 / % possible obs: 98.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 37.02 Å2 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.064 / Rrim(I) all: 0.175 / Χ2: 0.747 / Net I/σ(I): 3.5 / Num. measured all: 289070
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.12-2.24.30.58344580.7840.3030.660.48396.9
2.2-2.284.70.53845900.8120.2660.6020.50799.1
2.28-2.3950.45345790.8660.2140.5030.49899.3
2.39-2.515.10.43844600.890.2050.4860.49996.8
2.51-2.676.60.44945460.9280.180.4850.52698.4
2.67-2.887.40.39246260.960.1490.420.55299.8
2.88-3.177.60.28645850.9770.1080.3060.6199.6
3.17-3.627.10.17745420.9860.0710.1910.77698.2
3.62-4.567.70.12446330.9920.0470.1321.1699.4
4.56-307.50.09746490.9960.0370.1041.37798.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P7Y

7p7y


Resolution: 2.13→28.58 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 1988 4.38 %
Rwork0.1828 43363 -
obs0.1842 45351 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.75 Å2 / Biso mean: 41.2966 Å2 / Biso min: 24.12 Å2
Refinement stepCycle: final / Resolution: 2.13→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6892 0 0 339 7231
Biso mean---42.39 -
Num. residues----928
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2756X-RAY DIFFRACTION5.996TORSIONAL
12B2756X-RAY DIFFRACTION5.996TORSIONAL
13C2756X-RAY DIFFRACTION5.996TORSIONAL
14D2756X-RAY DIFFRACTION5.996TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.13-2.210.2491430.22073406354976
2.21-2.30.28332100.21834391460197
2.3-2.40.23861990.20244437463699
2.4-2.530.22432080.19974357456597
2.53-2.690.21741970.19234381457897
2.69-2.90.22992110.20334479469099
2.9-3.190.24492100.20334465467599
3.19-3.650.21892000.18554462466298
3.65-4.590.17842060.15794469467599
4.59-28.580.20592040.16784516472098

+
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