[English] 日本語
Yorodumi
- PDB-3qpm: Crystal structure of peroxiredoxin Prx4 from Pseudosciaena crocea -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qpm
TitleCrystal structure of peroxiredoxin Prx4 from Pseudosciaena crocea
ComponentsPeroxiredoxin
KeywordsOXIDOREDUCTASE / PEROXIREDOXIN / Thioredoxin fold / Peroxidase
Function / homology
Function and homology information


peroxiredoxin / peroxiredoxin activity / peroxidase activity
Similarity search - Function
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 speciesLarimichthys crocea (large yellow croaker)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLian, F.M. / Teng, Y.B. / Jiang, Y.L. / He, Y.X. / Chen, Y. / Zhou, C.Z.
CitationJournal: To be Published
Title: The N-terminal beta-sheet of peroxiredoxin Prx4 in the large yellow croaker Pseudosciaena crocea is critical for its peroxidase and anti-bacterial activities
Authors: Lian, F.M. / Mu, Y.N. / Teng, Y.B. / Ao, J.Q. / Jiang, Y.L. / He, Y.X. / Chen, Y.X. / Zhou, C.Z. / Chen, X.H.
History
DepositionFeb 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET Determination method: Author determined

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxiredoxin
B: Peroxiredoxin
C: Peroxiredoxin
D: Peroxiredoxin
E: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,44110
Polymers135,9805
Non-polymers4605
Water11,241624
1
A: Peroxiredoxin
B: Peroxiredoxin
C: Peroxiredoxin
D: Peroxiredoxin
E: Peroxiredoxin
hetero molecules

A: Peroxiredoxin
B: Peroxiredoxin
C: Peroxiredoxin
D: Peroxiredoxin
E: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,88120
Polymers271,96010
Non-polymers92110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area30130 Å2
ΔGint-199 kcal/mol
Surface area74480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.121, 195.998, 51.740
Angle α, β, γ (deg.)90.00, 105.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-348-

HOH

-
Components

#1: Protein
Peroxiredoxin


Mass: 27196.049 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Larimichthys crocea (large yellow croaker)
Plasmid: pET28a-derived / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: H3JQV8*PLUS, peroxiredoxin
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% polyethylene glycol monomethyl ether 5000, 0.1M HEPES-NaOH, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9999 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 108135 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.214 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PN8

2pn8


Resolution: 1.9→37.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21976 5372 5 %RANDOM
Rwork0.19561 ---
obs0.19682 102513 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.509 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å2-1.97 Å2
2---2.52 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7784 0 30 624 8438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228019
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.96410863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6165969
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30323.803355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.478151363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7891540
X-RAY DIFFRACTIONr_chiral_restr0.0930.21185
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216046
X-RAY DIFFRACTIONr_mcbond_it0.5461.54850
X-RAY DIFFRACTIONr_mcangle_it1.03727882
X-RAY DIFFRACTIONr_scbond_it1.64833169
X-RAY DIFFRACTIONr_scangle_it2.8144.52981
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 351 -
Rwork0.272 7124 -
obs--92.85 %

+
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