[English] 日本語
Yorodumi
- PDB-6gi8: Crystal structure of pentaerythritol tetranitrate reductase (PETN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gi8
TitleCrystal structure of pentaerythritol tetranitrate reductase (PETNR) mutant L25A
ComponentsPentaerythritol tetranitrate reductase
KeywordsFLAVOPROTEIN / Mutant L25A
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / FMN binding / cytosol
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilJ020192 United Kingdom
Biotechnology and Biological Sciences Research CouncilM007065 United Kingdom
Biotechnology and Biological Sciences Research CouncilH021523 United Kingdom
CitationJournal: Acs Catalysis / Year: 2018
Title: Nonequivalence of Second Sphere "Noncatalytic" Residues in Pentaerythritol Tetranitrate Reductase in Relation to Local Dynamics Linked to H-Transfer in Reactions with NADH and NADPH Coenzymes.
Authors: Iorgu, A.I. / Baxter, N.J. / Cliff, M.J. / Levy, C. / Waltho, J.P. / Hay, S. / Scrutton, N.S.
History
DepositionMay 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 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: Pentaerythritol tetranitrate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1143
Polymers40,5981
Non-polymers5152
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-3 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.808, 68.875, 88.874
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 Pentaerythritol tetranitrate reductase


Mass: 40598.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: onr / Production host: Escherichia coli (E. coli) / References: UniProt: P71278
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25 % (w/v) PEG 3000, 17 % (v/v) isopropanol, 0.1 M trisodium citrate, 0.1 M cacodylic acid (pH 6.5)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.42→54.44 Å / Num. obs: 66485 / % possible obs: 99.97 % / Redundancy: 8 % / Biso Wilson estimate: 14.71 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.03 / Rrim(I) all: 0.086 / Net I/σ(I): 15.88
Reflection shellResolution: 1.42→1.471 Å / Redundancy: 8 % / Rmerge(I) obs: 0.917 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 6534 / CC1/2: 0.682 / Rpim(I) all: 0.3435 / Rrim(I) all: 0.9803 / % possible all: 99.98

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ABA

2aba


Resolution: 1.42→54.44 Å / SU ML: 0.1491 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.9923
RfactorNum. reflection% reflectionSelection details
Rfree0.1824 3377 5.08 %Random
Rwork0.1323 ---
obs0.1349 66464 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.95 Å2
Refinement stepCycle: LAST / Resolution: 1.42→54.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 35 519 3319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01522959
X-RAY DIFFRACTIONf_angle_d1.36174040
X-RAY DIFFRACTIONf_chiral_restr0.1093436
X-RAY DIFFRACTIONf_plane_restr0.0122546
X-RAY DIFFRACTIONf_dihedral_angle_d17.61071096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.28681340.20812619X-RAY DIFFRACTION100
1.44-1.460.23081370.18722583X-RAY DIFFRACTION99.96
1.46-1.480.24321480.1772577X-RAY DIFFRACTION100
1.48-1.510.25111380.15682592X-RAY DIFFRACTION100
1.51-1.530.21811430.14312630X-RAY DIFFRACTION100
1.53-1.560.22611240.13272589X-RAY DIFFRACTION100
1.56-1.590.18671280.13032600X-RAY DIFFRACTION99.96
1.59-1.630.1921290.12412611X-RAY DIFFRACTION100
1.63-1.660.19671480.1182603X-RAY DIFFRACTION99.96
1.66-1.70.18221340.11252595X-RAY DIFFRACTION99.93
1.7-1.740.17521420.11182597X-RAY DIFFRACTION100
1.74-1.790.17311270.11812628X-RAY DIFFRACTION100
1.79-1.840.16971200.11862647X-RAY DIFFRACTION100
1.84-1.90.1831510.12432604X-RAY DIFFRACTION100
1.9-1.970.19271310.11972642X-RAY DIFFRACTION99.93
1.97-2.050.16981520.11782594X-RAY DIFFRACTION99.93
2.05-2.140.16351390.11662617X-RAY DIFFRACTION100
2.14-2.250.16781570.11242630X-RAY DIFFRACTION99.96
2.25-2.40.17081470.122629X-RAY DIFFRACTION99.93
2.4-2.580.17621320.1262662X-RAY DIFFRACTION100
2.58-2.840.22121590.13542636X-RAY DIFFRACTION99.93
2.84-3.250.17091680.14042640X-RAY DIFFRACTION99.93
3.25-4.10.16361460.13092718X-RAY DIFFRACTION99.83
4.1-54.480.17681430.15082844X-RAY DIFFRACTION99.93

+
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