[English] 日本語
Yorodumi
- PDB-7qw4: Pden_5119 protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qw4
TitlePden_5119 protein
ComponentsNADPH-dependent FMN reductase
KeywordsCYTOSOLIC PROTEIN / flavinreductase
Function / homology: / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavoprotein-like superfamily / oxidoreductase activity / NADPH-dependent FMN reductase
Function and homology information
Biological speciesParacoccus denitrificans PD1222 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKryl, M. / Sedlacek, V.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation16-18467S Czech Republic
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans .
Authors: Kryl, M. / Sedlacek, V. / Kucera, I.
History
DepositionJan 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 1, 2024Group: 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: NADPH-dependent FMN reductase
B: NADPH-dependent FMN reductase
C: NADPH-dependent FMN reductase
D: NADPH-dependent FMN reductase
E: NADPH-dependent FMN reductase
F: NADPH-dependent FMN reductase
G: NADPH-dependent FMN reductase
H: NADPH-dependent FMN reductase
I: NADPH-dependent FMN reductase
J: NADPH-dependent FMN reductase
K: NADPH-dependent FMN reductase
L: NADPH-dependent FMN reductase
M: NADPH-dependent FMN reductase
N: NADPH-dependent FMN reductase
O: NADPH-dependent FMN reductase
P: NADPH-dependent FMN reductase
Q: NADPH-dependent FMN reductase
R: NADPH-dependent FMN reductase
S: NADPH-dependent FMN reductase
T: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)412,56720
Polymers412,56720
Non-polymers00
Water00
1
A: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
Q: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
R: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
19
S: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
20
T: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)20,6281
Polymers20,6281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.510, 136.376, 212.314
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
NADPH-dependent FMN reductase


Mass: 20628.336 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans PD1222 (bacteria)
Gene: Pden_5119
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A1BCD5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM trisodium phosphate, 300 mM sodium chloride, 300 mM imidazole, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.06→49.1 Å / Num. obs: 65429 / % possible obs: 90.22 % / Redundancy: 2 % / Biso Wilson estimate: 81.63 Å2 / Rpim(I) all: 0.0603 / Net I/av σ(I): 2.26 / Net I/σ(I): 9.7
Reflection shellResolution: 3.06→3.14 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3022 / CC1/2: 0.794 / Rrim(I) all: 0.438 / % possible all: 57.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 3.1→48.75 Å / SU ML: 0.4076 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3212 2005 3.11 %
Rwork0.3201 62462 -
obs0.3202 64467 90.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.61 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26345 0 0 0 26345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013726958
X-RAY DIFFRACTIONf_angle_d2.093736588
X-RAY DIFFRACTIONf_chiral_restr0.17384135
X-RAY DIFFRACTIONf_plane_restr0.01644787
X-RAY DIFFRACTIONf_dihedral_angle_d21.19589124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.29281590.30094884X-RAY DIFFRACTION99.96
3.18-3.260.2791560.31584881X-RAY DIFFRACTION100
3.26-3.360.31461570.34144897X-RAY DIFFRACTION99.98
3.36-3.470.33481560.34884860X-RAY DIFFRACTION99.9
3.47-3.590.36841520.35474907X-RAY DIFFRACTION99.98
3.59-3.740.31641590.35054882X-RAY DIFFRACTION99.92
3.74-3.910.31151550.33754939X-RAY DIFFRACTION99.92
3.91-4.110.32391570.32714886X-RAY DIFFRACTION99.98
4.11-4.350.31661270.31243919X-RAY DIFFRACTION84.36
4.71-5.180.33181370.29964196X-RAY DIFFRACTION85.7
5.18-5.930.34091610.34374975X-RAY DIFFRACTION99.98
5.93-7.460.38941630.35255022X-RAY DIFFRACTION99.98
7.46-48.750.27431660.27135214X-RAY DIFFRACTION99.54

+
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