[English] 日本語
Yorodumi
- PDB-8y11: Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase bou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8y11
TitleCrystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase bound to NAD(H) and sulfate ion
ComponentsSDR family oxidoreductase
KeywordsOXIDOREDUCTASE / dehydrogenase / Rossmann Fold
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesHerbaspirillum huttiense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsAkagashi, M. / Watanabe, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2024
Title: Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase reveals a unique binding mode as a alpha-furanosyl hemiketal of substrates.
Authors: Akagashi, M. / Watanabe, S. / Kwiatkowski, S. / Drozak, J. / Terawaki, S. / Watanabe, Y.
History
DepositionJan 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,88522
Polymers110,3854
Non-polymers3,50018
Water8,359464
1
A: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5585
Polymers27,5961
Non-polymers9624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6806
Polymers27,5961
Non-polymers1,0845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7843
Polymers27,5961
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8628
Polymers27,5961
Non-polymers1,2667
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.337, 103.894, 133.058
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
SDR family oxidoreductase


Mass: 27596.275 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum huttiense (bacteria) / Gene: E2K99_19890 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0A4P7ABK7

-
Non-polymers , 6 types, 482 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris-HCl pH8.5, 25% PEG4000

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→48.39 Å / Num. obs: 220052 / % possible obs: 99.95 % / Redundancy: 19.84 % / CC1/2: 0.995 / Net I/σ(I): 16
Reflection shellResolution: 1.77→1.833 Å / Num. unique obs: 11338 / CC1/2: 0.584

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.77→48.39 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 10936 4.97 %
Rwork0.182 --
obs0.1834 220052 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7022 0 222 464 7708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167352
X-RAY DIFFRACTIONf_angle_d1.5359973
X-RAY DIFFRACTIONf_dihedral_angle_d10.7731069
X-RAY DIFFRACTIONf_chiral_restr0.0881190
X-RAY DIFFRACTIONf_plane_restr0.0121260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.790.37223690.37696974X-RAY DIFFRACTION100
1.79-1.810.38783460.36137012X-RAY DIFFRACTION100
1.81-1.830.36033330.33137040X-RAY DIFFRACTION100
1.83-1.860.30083440.30626946X-RAY DIFFRACTION100
1.86-1.880.29833580.29216970X-RAY DIFFRACTION100
1.88-1.910.29813950.27056926X-RAY DIFFRACTION100
1.91-1.930.26373530.24996950X-RAY DIFFRACTION100
1.93-1.960.28873630.23427059X-RAY DIFFRACTION100
1.96-1.990.24743960.22266877X-RAY DIFFRACTION100
1.99-2.030.2763940.21916973X-RAY DIFFRACTION100
2.03-2.060.2493690.21856956X-RAY DIFFRACTION100
2.06-2.10.24273280.21877011X-RAY DIFFRACTION100
2.1-2.140.26043570.22096951X-RAY DIFFRACTION100
2.14-2.180.21633890.196960X-RAY DIFFRACTION100
2.18-2.230.24263590.18186984X-RAY DIFFRACTION100
2.23-2.280.20933300.17567028X-RAY DIFFRACTION100
2.28-2.340.22773530.1776982X-RAY DIFFRACTION100
2.34-2.40.23083230.17996981X-RAY DIFFRACTION100
2.4-2.470.22193900.17486969X-RAY DIFFRACTION100
2.47-2.550.20683820.17226929X-RAY DIFFRACTION100
2.55-2.640.20273750.16976969X-RAY DIFFRACTION100
2.64-2.750.20223300.17346972X-RAY DIFFRACTION100
2.75-2.870.19373800.18366951X-RAY DIFFRACTION100
2.87-3.030.20134200.17226939X-RAY DIFFRACTION100
3.03-3.220.21973690.16176942X-RAY DIFFRACTION100
3.22-3.460.18073580.16237003X-RAY DIFFRACTION100
3.46-3.810.18894010.14736949X-RAY DIFFRACTION100
3.81-4.360.15993910.14536918X-RAY DIFFRACTION100
4.36-5.50.17943310.15567013X-RAY DIFFRACTION100
5.5-48.390.19013500.17996982X-RAY DIFFRACTION100

+
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