[English] 日本語
Yorodumi
- PDB-7nnx: E. coli NfsA with 1,4-benzoquinone -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nnx
TitleE. coli NfsA with 1,4-benzoquinone
ComponentsOxygen-insensitive NADPH nitroreductase
KeywordsOXIDOREDUCTASE / complex with benzoquinone substrate / flavoprotein / nitroreductase
Function / homology
Function and homology information


chromate reductase activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / cytosol
Similarity search - Function
Flavin oxidoreductase Frp family / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / benzene-1,4-diol / 1,4-benzoquinone / Oxygen-insensitive NADPH nitroreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDay, M.D. / Jarrom, D. / Hyde, E.I. / White, S.A.
CitationJournal: Biochem.J. / Year: 2021
Title: The structures of E. coli NfsA bound to the antibiotic nitrofurantoin; to 1,4-benzoquinone and to FMN.
Authors: Day, M.A. / Jarrom, D. / Christofferson, A.J. / Graziano, A.E. / Anderson, J.L.R. / Searle, P.F. / Hyde, E.I. / White, S.A.
History
DepositionFeb 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8079
Polymers26,8331
Non-polymers9748
Water4,648258
1
A: Oxygen-insensitive NADPH nitroreductase
hetero molecules

A: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,61418
Polymers53,6652
Non-polymers1,94916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14300 Å2
ΔGint-79 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.767, 51.963, 64.686
Angle α, β, γ (deg.)90.000, 133.920, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Oxygen-insensitive NADPH nitroreductase / Modulator of drug activity A


Mass: 26832.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cys90 has been modified by reaction with 1,4 benzoquinone to give a quinol adduct.
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: nfsA, mda18, mdaA, ybjB, b0851, JW0835 / Plasmid: pPS1341A1 / Details (production host): pET24 derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17117, Oxidoreductases

-
Non-polymers , 7 types, 266 molecules

#2: Chemical ChemComp-HQE / benzene-1,4-diol


Mass: 110.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PLQ / 1,4-benzoquinone / cyclohexa-2,5-diene-1,4-dione / QUINONE RING OF THE PLASTOQUINONE 9


Mass: 108.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18% PEG 3000, 100 mM Imidazole pH 7.0, 20% DMSO, 10 mM 1,4 Benzoquinone

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→46.59 Å / Num. obs: 23824 / % possible obs: 98.2 % / Redundancy: 11.4 % / Rsym value: 0.09 / Net I/σ(I): 24.8
Reflection shellResolution: 1.7→1.79 Å / Mean I/σ(I) obs: 4.6 / Num. unique obs: 3102 / Rsym value: 0.35 / % possible all: 88.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F5V

1f5v


Resolution: 1.7→46.59 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.527 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1699 1170 4.9 %RANDOM
Rwork0.1408 ---
obs0.1423 22647 98.19 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 80.55 Å2 / Biso mean: 17.844 Å2 / Biso min: 5.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å20.48 Å2
2---1.99 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.7→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 70 258 2203
Biso mean--18.05 26.54 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0172171
X-RAY DIFFRACTIONr_bond_other_d0.0010.0192060
X-RAY DIFFRACTIONr_angle_refined_deg1.261.8692968
X-RAY DIFFRACTIONr_angle_other_deg1.0892.6614750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29322.261115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95515364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8021516
X-RAY DIFFRACTIONr_chiral_restr0.080.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022561
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02501
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 64 -
Rwork0.194 1417 -
all-1481 -
obs--83.63 %
Refinement TLS params.Method: refined / Origin x: 3.99 Å / Origin y: -25.466 Å / Origin z: 7.214 Å
111213212223313233
T0.0779 Å2-0.0053 Å2-0.0225 Å2-0.1207 Å2-0.0007 Å2--0.0084 Å2
L0.7091 °2-0.0844 °20.1476 °2-0.3334 °20.0483 °2--1.2884 °2
S-0.0353 Å °-0.097 Å °0.0218 Å °0.065 Å °0.0078 Å °-0.0199 Å °-0.1511 Å °0.0541 Å °0.0276 Å °

+
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