[English] 日本語
Yorodumi
- PDB-7t2z: The structure of Haemophilus influenzae Rd KW20 nitroreductase co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t2z
TitleThe structure of Haemophilus influenzae Rd KW20 nitroreductase complexed with 1-methyl-5-nitroimidazole
ComponentsPutative NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / Nitroreductase / Haemophilus influenzae / 1-methyl-5-nitroimidazole
Function / homology
Function and homology information


: / 2,4,6-trinitrotoluene catabolic process / Oxidoreductases / cytosol
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
ACETIC ACID / 1-methyl-5-nitro-1H-imidazole / FLAVIN MONONUCLEOTIDE / Putative NAD(P)H nitroreductase
Similarity search - Component
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2547 Å
AuthorsWanniarachchi, T.N. / Bruner, S.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Chem Biol / Year: 2022
Title: Biochemical and structural characterization of Haemophilus influenzae nitroreductase in metabolizing nitroimidazoles.
Authors: Liu, D. / Wanniarachchi, T.N. / Jiang, G. / Seabra, G. / Cao, S. / Bruner, S.D. / Ding, Y.
History
DepositionDec 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative NAD(P)H nitroreductase
B: Putative NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7198
Polymers53,4952
Non-polymers1,2246
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-47 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.315, 57.315, 121.007
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Putative NAD(P)H nitroreductase


Mass: 26747.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: HI_1278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57431, Oxidoreductases

-
Non-polymers , 5 types, 91 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-EIV / 1-methyl-5-nitro-1H-imidazole


Mass: 127.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 8% v/v tacsimateTM pH 5.0 and 20% w/v polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.2547→49.6481 Å / Num. obs: 20949 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.976 / CC star: 0.994 / Net I/σ(I): 7.82
Reflection shellResolution: 2.2547→2.3736 Å / Redundancy: 5 % / Num. unique obs: 2086 / CC1/2: 0.636 / CC star: 0.882 / % possible all: 99.05

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WT2

6wt2


Resolution: 2.2547→49.6481 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 970 4.63 %RANDOM
Rwork0.1784 19980 --
obs0.1804 20949 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.71 Å2 / Biso mean: 46.2929 Å2 / Biso min: 22.95 Å2
Refinement stepCycle: final / Resolution: 2.2547→49.6481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 83 85 3684
Biso mean--39.5 46.84 -
Num. residues----438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2547-2.37360.34341490.2632847299699
2.3736-2.52230.26831380.235828472985100
2.5223-2.7170.30211230.22328542977100
2.717-2.99040.25171500.213928523002100
2.9904-3.42310.25741300.190728692999100
3.4231-4.31230.1921390.154428663005100
4.3123-49.64810.17521410.144828452986100

+
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