[English] 日本語
Yorodumi
- PDB-4y9i: Structure of F420-H2 Dependent Reductase (FDR-A) msmeg_2027 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y9i
TitleStructure of F420-H2 Dependent Reductase (FDR-A) msmeg_2027
ComponentsMycobacterium tuberculosis paralogous family 11
KeywordsOXIDOREDUCTASE / F420 / quinone / reductase
Function / homology
Function and homology information


coenzyme F420 binding / oxidoreductase activity / plasma membrane
Similarity search - Function
F420H(2)-dependent quinone reductase / F420H(2)-dependent quinone reductase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Nitroreductase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.498 Å
AuthorsAhmed, F.H. / Carr, P.D. / Jackson, C.J.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria.
Authors: Ahmed, F.H. / Carr, P.D. / Lee, B.M. / Afriat-Jurnou, L. / Mohamed, A.E. / Hong, N.S. / Flanagan, J. / Taylor, M.C. / Greening, C. / Jackson, C.J.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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: Mycobacterium tuberculosis paralogous family 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1172
Polymers13,0221
Non-polymers951
Water3,387188
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)37.490, 36.850, 77.591
Angle α, β, γ (deg.)90.00, 96.59, 90.00
Int Tables number5
Space group name H-MI121
DetailsMonomer confirmed by gel filtration

-
Components

#1: Protein Mycobacterium tuberculosis paralogous family 11 / Nitroreductase / Uncharacterized protein


Mass: 13021.810 Da / Num. of mol.: 1 / Fragment: UNP Residues 27-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2027, MSMEI_1982, LJ00_10110 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QU01
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 20% PEGMME5000, 0.05 M imidazole

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.498→26.195 Å / Num. obs: 16332 / % possible obs: 95.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 13
Reflection shellResolution: 1.498→1.52 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.1 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R5Z

3r5z


Resolution: 1.498→26.195 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 1625 5.13 %RANDOM
Rwork0.155 16330 --
obs0.1571 16330 95.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.498→26.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 0 188 1112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021013
X-RAY DIFFRACTIONf_angle_d1.9091388
X-RAY DIFFRACTIONf_dihedral_angle_d14.815384
X-RAY DIFFRACTIONf_chiral_restr0.178145
X-RAY DIFFRACTIONf_plane_restr0.013184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.498-1.54210.3341420.26742374X-RAY DIFFRACTION92
1.5421-1.59190.29141690.23142416X-RAY DIFFRACTION94
1.5919-1.64880.24191440.20462495X-RAY DIFFRACTION94
1.6488-1.71480.23121300.19062455X-RAY DIFFRACTION95
1.7148-1.79280.28151130.17622526X-RAY DIFFRACTION96
1.7928-1.88730.2381170.15412541X-RAY DIFFRACTION96
1.8873-2.00550.20641310.1452531X-RAY DIFFRACTION97
2.0055-2.16030.20061570.1552559X-RAY DIFFRACTION97
2.1603-2.37750.2381230.15062592X-RAY DIFFRACTION98
2.3775-2.72120.15211280.1482546X-RAY DIFFRACTION98
2.7212-3.42730.16521310.13882586X-RAY DIFFRACTION97
3.4273-26.19850.15041400.12662457X-RAY DIFFRACTION94

+
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