[English] 日本語
Yorodumi
- PDB-6ac4: Rat Xanthine oxidoreductase, D428N variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ac4
TitleRat Xanthine oxidoreductase, D428N variant
ComponentsXanthine dehydrogenase/oxidase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / Azathioprine ADME / Purine catabolism / guanine catabolic process / deoxyguanosine catabolic process / xanthine dehydrogenase / xanthine oxidase ...Butyrophilin (BTN) family interactions / hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / Azathioprine ADME / Purine catabolism / guanine catabolic process / deoxyguanosine catabolic process / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / GMP catabolic process / deoxyinosine catabolic process / deoxyadenosine catabolic process / dAMP catabolic process / inosine catabolic process / regulation of epithelial cell differentiation / response to azide / AMP catabolic process / dGMP catabolic process / amide catabolic process / adenosine catabolic process / response to aluminum ion / IMP catabolic process / allantoin metabolic process / response to carbon monoxide / molybdopterin cofactor binding / nitrite reductase (NO-forming) activity / iron-sulfur cluster assembly / cellular response to interleukin-1 / lactation / FAD binding / sarcoplasmic reticulum / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / cellular response to tumor necrosis factor / peroxisome / flavin adenine dinucleotide binding / response to lipopolysaccharide / oxidoreductase activity / iron ion binding / protein homodimerization activity / extracellular space / identical protein binding / cytosol
Similarity search - Function
Xanthine dehydrogenase, small subunit / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal ...Xanthine dehydrogenase, small subunit / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / CO dehydrogenase flavoprotein, C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Aldehyde Oxidoreductase; domain 3 / FAD-binding, type PCMH, subdomain 1 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / Enolase-like; domain 1 / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / DNA polymerase; domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Xanthine dehydrogenase/oxidase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsOkamoto, K. / Kawaguchi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
15H04702 Japan
CitationJournal: To Be Published
Title: Rat Xanthine oxidoreductase, D428A variant, NAD bound form
Authors: Okamoto, K. / Kawaguchi, Y.
History
DepositionJul 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xanthine dehydrogenase/oxidase
B: Xanthine dehydrogenase/oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,1018
Polymers292,8272
Non-polymers2,2746
Water28,2481568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-107 kcal/mol
Surface area86270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.296, 138.648, 221.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Xanthine dehydrogenase/oxidase


Mass: 146413.375 Da / Num. of mol.: 2 / Mutation: D428N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Xdh / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P22985, xanthine dehydrogenase, xanthine oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1568 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 9-11% polyethylene glycol 8000, 0.6M Li2SO4, 5mM DTT, 1mM sodium salicylate, 0.4mM EDTA, 15% glycerol, 40mM HEPES (pH 6.20), VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→39.63 Å / Num. obs: 162134 / % possible obs: 98.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 17.5
Reflection shellResolution: 2.19→2.247 Å / Rmerge(I) obs: 0.416 / Num. unique obs: 26792

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WYG

1wyg


Resolution: 2.19→39.63 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.717 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 7313 5.1 %RANDOM
Rwork0.17459 ---
obs0.17764 135743 91.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.509 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.19→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20002 0 122 1568 21692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01420554
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718686
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.66727825
X-RAY DIFFRACTIONr_angle_other_deg0.91.63443878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23552583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52122.231995
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.904153541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.10715127
X-RAY DIFFRACTIONr_chiral_restr0.0690.22712
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222990
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023712
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_it2.3833.21610350
X-RAY DIFFRACTIONr_mcbond_other2.3823.21510349
X-RAY DIFFRACTIONr_mcangle_it3.5034.81212927
X-RAY DIFFRACTIONr_mcangle_other3.5034.81312928
X-RAY DIFFRACTIONr_scbond_it2.8473.5510204
X-RAY DIFFRACTIONr_scbond_other2.8483.55110197
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3285.18814887
X-RAY DIFFRACTIONr_long_range_B_refined18.59339.94223759
X-RAY DIFFRACTIONr_long_range_B_other18.25639.63123405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 584 -
Rwork0.22 9889 -
obs--91.78 %

+
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