[English] 日本語
Yorodumi
- PDB-5via: Crystal structural of Leishmania major pseudoperoxidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5via
TitleCrystal structural of Leishmania major pseudoperoxidase
ComponentsPseudoperoxidase
KeywordsOXIDOREDUCTASE / heme protein / peroxidase
Function / homology
Function and homology information


response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / cellular response to oxidative stress / heme binding / metal ion binding / membrane
Similarity search - Function
Heme-binding peroxidase Ccp1-like / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Haem peroxidase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Plant heme peroxidase family profile domain-containing protein
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.764 Å
AuthorsChreifi, G. / Dejam, D. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM57353 United States
CitationJournal: J. Biol. Inorg. Chem. / Year: 2017
Title: Crystal structure and functional analysis of Leishmania major pseudoperoxidase.
Authors: Chreifi, G. / Dejam, D. / Poulos, T.L.
History
DepositionApr 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pseudoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6832
Polymers33,0661
Non-polymers6161
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.680, 63.680, 152.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-757-

HOH

-
Components

#1: Protein Pseudoperoxidase / Uncharacterized protein


Mass: 33066.293 Da / Num. of mol.: 1 / Fragment: UNP residues 49-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_21_1567 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4QC30
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14 mg/mL protein, 5% 2-methyl-2,4-pentanediol, 10% polyethylene glycol 6000, and 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Dec 16, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 1.76→48.88 Å / Num. obs: 31236 / % possible obs: 98.22 % / Redundancy: 18 % / Biso Wilson estimate: 34.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.049 / Net I/σ(I): 73.11
Reflection shellResolution: 1.76→1.83 Å / Redundancy: 16.5 % / Num. unique obs: 3100 / CC1/2: 0.297 / % possible all: 94.03

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
iMOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.764→48.875 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 1522 4.86 %Random selection
Rwork0.1957 ---
obs0.1969 31200 98.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.764→48.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 43 181 2429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072309
X-RAY DIFFRACTIONf_angle_d1.0483149
X-RAY DIFFRACTIONf_dihedral_angle_d14.239844
X-RAY DIFFRACTIONf_chiral_restr0.065341
X-RAY DIFFRACTIONf_plane_restr0.005405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.764-1.79450.42221340.40082632X-RAY DIFFRACTION95
1.7945-1.82710.37191680.37532635X-RAY DIFFRACTION94
1.8271-1.86220.34451270.3712672X-RAY DIFFRACTION95
1.8622-1.90030.33751570.34172658X-RAY DIFFRACTION95
1.9003-1.94160.382860.3312763X-RAY DIFFRACTION97
1.9416-1.98670.29361370.31082764X-RAY DIFFRACTION97
1.9867-2.03640.28621210.28172735X-RAY DIFFRACTION97
2.0364-2.09150.29971280.26432774X-RAY DIFFRACTION98
2.0915-2.1530.28841730.24282728X-RAY DIFFRACTION99
2.153-2.22250.26581610.23532756X-RAY DIFFRACTION99
2.2225-2.3020.29911460.22912788X-RAY DIFFRACTION100
2.302-2.39410.20231380.21732805X-RAY DIFFRACTION100
2.3941-2.50310.26551310.20012816X-RAY DIFFRACTION100
2.5031-2.6350.17041450.17982800X-RAY DIFFRACTION100
2.635-2.80010.23081300.18012825X-RAY DIFFRACTION100
2.8001-3.01630.19861440.17782812X-RAY DIFFRACTION100
3.0163-3.31980.23271360.17062808X-RAY DIFFRACTION100
3.3198-3.80.16071440.15662799X-RAY DIFFRACTION100
3.8-4.78690.17381650.15112787X-RAY DIFFRACTION100
4.7869-48.89410.20971470.18742798X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 32.8372 Å / Origin y: 41.2282 Å / Origin z: 60.1489 Å
111213212223313233
T0.1681 Å20.0055 Å2-0.0109 Å2-0.2404 Å20.0527 Å2--0.1655 Å2
L2.6912 °20.1807 °20.6496 °2-1.7126 °20.3026 °2--2.4513 °2
S-0.0276 Å °0.311 Å °0.1501 Å °-0.1645 Å °0.0506 Å °0.0278 Å °0.1125 Å °0.0848 Å °-0.0224 Å °
Refinement TLS groupSelection details: (chain A and resid 56:333)

+
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