[English] 日本語
Yorodumi
- PDB-4ynu: Crystal structure of Aspergillus flavus FADGDH in complex with D-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ynu
TitleCrystal structure of Aspergillus flavus FADGDH in complex with D-glucono-1,5-lactone
ComponentsGlucose oxidase, putative
KeywordsOXIDOREDUCTASE / Glucose dehydrogenase / FAD
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Glucose Oxidase, domain 2 / GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / D-glucono-1,5-lactone / Glucose oxidase, putative
Similarity search - Component
Biological speciesAspergillus flavus NRRL3357 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsYoshida, H. / Sakai, G. / Kojima, K. / Kamitori, S. / Sode, K.
CitationJournal: Sci Rep / Year: 2015
Title: Structural analysis of fungus-derived FAD glucose dehydrogenase
Authors: Yoshida, H. / Sakai, G. / Mori, K. / Kojima, K. / Kamitori, S. / Sode, K.
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucose oxidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6914
Polymers61,5491
Non-polymers1,1423
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-9 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.658, 64.877, 75.889
Angle α, β, γ (deg.)90.000, 100.460, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glucose oxidase, putative / Glucose dehydrogenase


Mass: 61548.922 Da / Num. of mol.: 1 / Fragment: UNP residues 24-593
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus NRRL3357 (mold) / Strain: NRRL 3357 / Gene: AFLA_076820 / Plasmid: pET30c / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2(DE3) / References: UniProt: B8MX95, EC: 1.1.5.9
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Sugar ChemComp-LGC / D-glucono-1,5-lactone / (3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE / GLUCONOLACTONE


Type: D-saccharide / Mass: 178.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BisTris, 20-25 % PEG 3350 / PH range: 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 65992 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Χ2: 1.082 / Net I/av σ(I): 21.517 / Net I/σ(I): 10.6 / Num. measured all: 242808
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.57-1.630.4832210.84497.6
1.6-1.633.60.44632650.894100
1.63-1.663.70.39533270.93100
1.66-1.693.70.33632870.948100
1.69-1.733.70.29432650.973100
1.73-1.773.70.25133021.023100
1.77-1.813.70.22432961.084100
1.81-1.863.70.17932501.044100
1.86-1.923.70.15133111.169100
1.92-1.983.70.12732891.22999.9
1.98-2.053.70.10432961.074100
2.05-2.133.70.08732731.13299.9
2.13-2.233.70.07533221.107100
2.23-2.353.80.06832851.09100
2.35-2.493.80.06133241.091100
2.49-2.683.70.05732751.109100
2.68-2.953.70.05633471.312100
2.95-3.383.70.05333091.21199.9
3.38-4.263.60.03933351.145100
4.26-503.70.0334131.14899.9

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALEPACKdata reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CF3

1cf3


Resolution: 1.57→39.02 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.381 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1642 3347 5.1 %RANDOM
Rwork0.1407 ---
obs0.1419 62625 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.89 Å2 / Biso mean: 20.571 Å2 / Biso min: 6.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.57→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4324 0 77 431 4832
Biso mean--21.06 28.07 -
Num. residues----569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194614
X-RAY DIFFRACTIONr_bond_other_d00.024349
X-RAY DIFFRACTIONr_angle_refined_deg1.1231.9716316
X-RAY DIFFRACTIONr_angle_other_deg0.642310007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3165600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5624.532203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1815731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.041527
X-RAY DIFFRACTIONr_chiral_restr0.0790.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215336
X-RAY DIFFRACTIONr_gen_planes_other00.021063
LS refinement shellResolution: 1.571→1.612 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 243 -
Rwork0.222 4477 -
all-4720 -
obs--96.64 %

+
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://pdbjlvh1.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