[English] 日本語
Yorodumi
- PDB-6khx: Crystal structure of Prx from Akkermansia muciniphila -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6khx
TitleCrystal structure of Prx from Akkermansia muciniphila
ComponentsPeroxiredoxin
KeywordsOXIDOREDUCTASE / Peroxiredoxins / Akkermansia muciniphila / Crystal structure / peroxidase activity
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsLi, M. / Wang, J. / Xu, W. / Wang, Y. / Zhang, M. / Wang, M.
CitationJournal: Febs Lett. / Year: 2020
Title: Crystal structure of Akkermansia muciniphila peroxiredoxin reveals a novel regulatory mechanism of typical 2-Cys Prxs by a distinct loop.
Authors: Li, M. / Wang, J. / Xu, W. / Wang, Y. / Zhang, M. / Wang, M.
History
DepositionJul 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: 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
Revision 1.2Nov 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxiredoxin
B: Peroxiredoxin
C: Peroxiredoxin
D: Peroxiredoxin
E: Peroxiredoxin
F: Peroxiredoxin
G: Peroxiredoxin
H: Peroxiredoxin
I: Peroxiredoxin
J: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,53918
Polymers239,21910
Non-polymers3218
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34250 Å2
ΔGint-280 kcal/mol
Surface area76220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.733, 211.371, 92.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 120 or resid 127 through 208))
21(chain B and (resid 1 through 120 or resid 127 through 208))
31(chain C and (resid 1 through 120 or resid 127 through 208))
41(chain D and (resid 1 through 120 or resid 127 through 208))
51(chain E and (resid 1 through 120 or resid 127 through 208))
61(chain F and (resid 1 through 120 or resid 127 through 208))
71(chain G and (resid 1 through 120 or resid 127 through 208))
81(chain H and resid 1 through 208)
91(chain I and (resid 1 through 120 or resid 127 through 208))
101(chain J and (resid 1 through 120 or resid 127 through 208))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLU(chain A and (resid 1 through 120 or resid 127 through 208))AA1 - 1201 - 120
12ASNASNLEULEU(chain A and (resid 1 through 120 or resid 127 through 208))AA127 - 208127 - 208
21METMETGLUGLU(chain B and (resid 1 through 120 or resid 127 through 208))BB1 - 1201 - 120
22ASNASNLEULEU(chain B and (resid 1 through 120 or resid 127 through 208))BB127 - 208127 - 208
31METMETGLUGLU(chain C and (resid 1 through 120 or resid 127 through 208))CC1 - 1201 - 120
32ASNASNLEULEU(chain C and (resid 1 through 120 or resid 127 through 208))CC127 - 208127 - 208
41METMETGLUGLU(chain D and (resid 1 through 120 or resid 127 through 208))DD1 - 1201 - 120
42ASNASNLEULEU(chain D and (resid 1 through 120 or resid 127 through 208))DD127 - 208127 - 208
51METMETGLUGLU(chain E and (resid 1 through 120 or resid 127 through 208))EE1 - 1201 - 120
52ASNASNLEULEU(chain E and (resid 1 through 120 or resid 127 through 208))EE127 - 208127 - 208
61METMETGLUGLU(chain F and (resid 1 through 120 or resid 127 through 208))FF1 - 1201 - 120
62ASNASNLEULEU(chain F and (resid 1 through 120 or resid 127 through 208))FF127 - 208127 - 208
71METMETGLUGLU(chain G and (resid 1 through 120 or resid 127 through 208))GG1 - 1201 - 120
72ASNASNLEULEU(chain G and (resid 1 through 120 or resid 127 through 208))GG127 - 208127 - 208
81METMETLEULEU(chain H and resid 1 through 208)HH1 - 2081 - 208
91METMETGLUGLU(chain I and (resid 1 through 120 or resid 127 through 208))II1 - 1201 - 120
92ASNASNLEULEU(chain I and (resid 1 through 120 or resid 127 through 208))II127 - 208127 - 208
101METMETGLUGLU(chain J and (resid 1 through 120 or resid 127 through 208))JJ1 - 1201 - 120
102ASNASNLEULEU(chain J and (resid 1 through 120 or resid 127 through 208))JJ127 - 208127 - 208

-
Components

#1: Protein
Peroxiredoxin / Prx


Mass: 23921.850 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: CXU17_12910, CXU19_10505 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N8HPY4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Sodium citrate pH 5.0, 0.06 M CaCl2, 30% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 81798 / % possible obs: 99.4 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.027 / Rrim(I) all: 0.098 / Χ2: 0.962 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6913.31.00980920.880.2821.0490.85899.7
2.69-2.813.40.66680810.9410.1860.6920.8899.8
2.8-2.9313.40.45981310.9690.1290.4770.9199.9
2.93-3.0813.20.29481330.9840.0830.3060.96899.8
3.08-3.2812.60.280340.990.0580.2091.02698.6
3.28-3.5313.60.13881780.9950.0380.1431.08499.7
3.53-3.8813.90.10482100.9960.0290.1081.098100
3.88-4.4513.40.07982170.9970.0220.0821.0799.6
4.45-5.613.20.06781830.9970.0190.070.9498.4
5.6-50130.05785390.9970.0170.0590.78298.9

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I81

2i81


Resolution: 2.58→49.095 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.81
RfactorNum. reflection% reflection
Rfree0.218 3981 5.02 %
Rwork0.1768 --
obs0.179 79345 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.49 Å2 / Biso mean: 42.8824 Å2 / Biso min: 16.14 Å2
Refinement stepCycle: final / Resolution: 2.58→49.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16325 0 8 621 16954
Biso mean--76.89 37.82 -
Num. residues----2089
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9629X-RAY DIFFRACTION8.004TORSIONAL
12B9629X-RAY DIFFRACTION8.004TORSIONAL
13C9629X-RAY DIFFRACTION8.004TORSIONAL
14D9629X-RAY DIFFRACTION8.004TORSIONAL
15E9629X-RAY DIFFRACTION8.004TORSIONAL
16F9629X-RAY DIFFRACTION8.004TORSIONAL
17G9629X-RAY DIFFRACTION8.004TORSIONAL
18H9629X-RAY DIFFRACTION8.004TORSIONAL
19I9629X-RAY DIFFRACTION8.004TORSIONAL
110J9629X-RAY DIFFRACTION8.004TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.58-2.61430.3404890.2482166961
2.6143-2.64740.31831200.2547221480
2.6474-2.68220.30771110.2362237786
2.6822-2.71890.27421310.2333249090
2.7189-2.75780.32651260.2442260194
2.7578-2.79890.30531240.2342268096
2.7989-2.84270.28931480.2329273299
2.8427-2.88930.30531810.2267275199
2.8893-2.93910.24971340.2252272199
2.9391-2.99250.29721470.21852799100
2.9925-3.05010.2741560.21272730100
3.0501-3.11230.25081290.20412804100
3.1123-3.180.22761260.2053276799
3.18-3.25390.2421350.2082270297
3.2539-3.33530.2731410.2158275999
3.3353-3.42550.28041560.20322800100
3.4255-3.52620.25051510.19112774100
3.5262-3.640.21671310.19182792100
3.64-3.77010.25041600.18182789100
3.7701-3.9210.18381440.16182814100
3.921-4.09930.17411550.1445277899
4.0993-4.31530.18181480.13982800100
4.3153-4.58550.19241400.12932830100
4.5855-4.93930.14761660.13270096
4.9393-5.43570.16911640.13272816100
5.4357-6.2210.18481550.16752858100
6.221-7.83260.18161580.16012885100
7.8326-490.16581550.1445293297

+
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