[English] 日本語
Yorodumi
- PDB-28db: Crystal structure of the thioredoxin domain of Amuc_2173 from Akk... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 28db
TitleCrystal structure of the thioredoxin domain of Amuc_2173 from Akkermansia muciniphila
ComponentsRedoxin domain protein
KeywordsOXIDOREDUCTASE / thioredoxin / Akkermansia muciniphila / Amuc_2173 / CXXC
Function / homology
Function and homology information


cytochrome complex assembly / cell envelope / oxidoreductase activity
Similarity search - Function
: / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Redoxin domain protein
Similarity search - Component
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.575 Å
AuthorsWei, J. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2026
Title: Functional and structural characterization of Akkermansia muciniphila thioredoxin domain-containing protein Amuc_2173
Authors: Wei, J. / Zhang, R. / Xiao, Z. / Li, Q. / Wang, M.
History
DepositionJun 22, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Redoxin domain protein
B: Redoxin domain protein


Theoretical massNumber of molelcules
Total (without water)36,0902
Polymers36,0902
Non-polymers00
Water5,981332
1
A: Redoxin domain protein


Theoretical massNumber of molelcules
Total (without water)18,0451
Polymers18,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Redoxin domain protein


Theoretical massNumber of molelcules
Total (without water)18,0451
Polymers18,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.662, 44.534, 45.714
Angle α, β, γ (deg.)93.24, 110.14, 114.86
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Redoxin domain protein


Mass: 18044.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria)
Gene: Amuc_2173 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: B2UPV2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 30.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 7.5, and 24% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 32585 / % possible obs: 95.6 % / Redundancy: 3.5 % / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.047 / Rrim(I) all: 0.089 / Χ2: 0.858 / Net I/σ(I): 8.5 / Num. measured all: 115089
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.57-1.633.30.35930070.8770.9670.2360.4321.01288.7
1.63-1.693.70.29732260.9370.9840.1790.3470.9995.1
1.69-1.773.60.21332810.9510.9870.1310.250.94595
1.77-1.863.50.15632400.9690.9920.0980.1840.96295.6
1.86-1.983.60.12732860.9770.9940.0770.1490.93996.2
1.98-2.133.50.09732540.9850.9960.060.1140.85396
2.13-2.353.50.07933090.9880.9970.0490.0930.80796.4
2.35-2.683.60.06733220.9890.9970.0410.0790.65797.2
2.68-3.383.60.0733160.9860.9970.0430.0820.72898
3.38-503.50.06633440.9850.9960.0420.0790.71697.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.575→41.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.535 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19553 1694 5.3 %RANDOM
Rwork0.15445 ---
obs0.15655 30502 94.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.732 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å2-0.4 Å20.23 Å2
2--0.01 Å20.1 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.575→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 0 332 2476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122299
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162235
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.8613126
X-RAY DIFFRACTIONr_angle_other_deg0.5411.7625240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7725297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.32253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5110424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022573
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
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_it4.1071.4551116
X-RAY DIFFRACTIONr_mcbond_other4.0881.4551116
X-RAY DIFFRACTIONr_mcangle_it6.582.6081398
X-RAY DIFFRACTIONr_mcangle_other6.5812.611399
X-RAY DIFFRACTIONr_scbond_it4.3821.621183
X-RAY DIFFRACTIONr_scbond_other4.3811.6211184
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6432.8651716
X-RAY DIFFRACTIONr_long_range_B_refined12.5812153.6910029
X-RAY DIFFRACTIONr_long_range_B_other12.7022242.359623
X-RAY DIFFRACTIONr_rigid_bond_restr2.98534534
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.575→1.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 104 -
Rwork0.217 1799 -
obs--77.04 %

+
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