[English] 日本語
Yorodumi
- PDB-8qc8: Crystal structure of NAD-dependent glycoside hydrolase from Flavo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qc8
TitleCrystal structure of NAD-dependent glycoside hydrolase from Flavobacterium sp. (strain K172) in complex with co-factor NAD+
ComponentsGfo/Idh/MocA family oxidoreductase
KeywordsHYDROLASE / oxidoreductive / sulfoquinovose / glycoside hydrolase
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / :
Function and homology information
Biological speciesPaenarthrobacter ureafaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPickles, I.B. / Sharma, M. / Davies, G.J.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)951231European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W003805/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Widespread Family of NAD + -Dependent Sulfoquinovosidases at the Gateway to Sulfoquinovose Catabolism.
Authors: Kaur, A. / Pickles, I.B. / Sharma, M. / Madeido Soler, N. / Scott, N.E. / Pidot, S.J. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.
History
DepositionAug 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Gfo/Idh/MocA family oxidoreductase
C: Gfo/Idh/MocA family oxidoreductase
D: Gfo/Idh/MocA family oxidoreductase
A: Gfo/Idh/MocA family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,74914
Polymers171,5254
Non-polymers3,22410
Water4,504250
1
B: Gfo/Idh/MocA family oxidoreductase
C: Gfo/Idh/MocA family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4698
Polymers85,7632
Non-polymers1,7076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-56 kcal/mol
Surface area26390 Å2
MethodPISA
2
D: Gfo/Idh/MocA family oxidoreductase
A: Gfo/Idh/MocA family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2796
Polymers85,7632
Non-polymers1,5174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-56 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.775, 161.490, 175.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Gfo/Idh/MocA family oxidoreductase


Mass: 42881.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter ureafaciens (bacteria)
Gene: FV140_09610 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7D7VZ79
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM bis-tris propane pH 7, 0.02 mM sodium and potassium phosphate, 28% (w/v) PEG3350, 1 mM MnCl2, 5 mM NAD+

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.35→59.45 Å / Num. obs: 63829 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.055 / Rrim(I) all: 0.2 / Χ2: 0.92 / Net I/σ(I): 8 / Num. measured all: 830971
Reflection shellResolution: 2.35→2.41 Å / % possible obs: 97.8 % / Redundancy: 10.2 % / Rmerge(I) obs: 1.779 / Num. measured all: 44513 / Num. unique obs: 4352 / CC1/2: 0.933 / Rpim(I) all: 0.573 / Rrim(I) all: 1.874 / Χ2: 0.86 / Net I/σ(I) obs: 1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→59.45 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 14.836 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R: 0.468 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27837 3257 5.1 %RANDOM
Rwork0.22852 ---
obs0.23112 60510 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.444 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å20 Å20 Å2
2---9.04 Å2-0 Å2
3---5.6 Å2
Refinement stepCycle: 1 / Resolution: 2.35→59.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10823 0 206 250 11279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01211274
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610325
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.65715384
X-RAY DIFFRACTIONr_angle_other_deg0.4441.57423755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03651428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.918567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.853101702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.21776
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022408
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4725.5945730
X-RAY DIFFRACTIONr_mcbond_other5.4725.5945730
X-RAY DIFFRACTIONr_mcangle_it8.06110.0437152
X-RAY DIFFRACTIONr_mcangle_other8.06110.0437153
X-RAY DIFFRACTIONr_scbond_it5.5045.7795544
X-RAY DIFFRACTIONr_scbond_other5.5035.7795545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.02210.4838233
X-RAY DIFFRACTIONr_long_range_B_refined10.63651.7911875
X-RAY DIFFRACTIONr_long_range_B_other10.63651.7911876
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 215 -
Rwork0.422 4337 -
obs--97.51 %

+
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