[English] 日本語
Yorodumi
- PDB-5krd: Crystal structure of haliscomenobacter hydrossis iodotyrosine dei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5krd
TitleCrystal structure of haliscomenobacter hydrossis iodotyrosine deiodinase (IYD) bound to FMN and 2-iodophenol (2IP)
ComponentsNitroreductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


iodotyrosine deiodinase / iodotyrosine deiodinase activity / FMN binding
Similarity search - Function
NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-iodanylphenol / FLAVIN MONONUCLEOTIDE / Iodotyrosine deiodinase
Similarity search - Component
Biological speciesHaliscomenobacter hydrossis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsIngavat, N. / Kavran, J.M. / Sun, Z. / Rokita, S.
CitationJournal: Biochemistry / Year: 2017
Title: Active Site Binding Is Not Sufficient for Reductive Deiodination by Iodotyrosine Deiodinase.
Authors: Ingavat, N. / Kavran, J.M. / Sun, Z. / Rokita, S.E.
History
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Data collection / Database references
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Oct 4, 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: Nitroreductase
B: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6856
Polymers52,3322
Non-polymers1,3534
Water2,270126
1
A: Nitroreductase
hetero molecules

A: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6856
Polymers52,3322
Non-polymers1,3534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area11320 Å2
ΔGint-77 kcal/mol
Surface area17570 Å2
MethodPISA
2
B: Nitroreductase
hetero molecules

B: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6856
Polymers52,3322
Non-polymers1,3534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area11370 Å2
ΔGint-75 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.049, 155.049, 89.005
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

21B-415-

HOH

-
Components

#1: Protein Nitroreductase /


Mass: 26165.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliscomenobacter hydrossis (strain ATCC 27775 / DSM 1100 / LMG 10767 / O) (bacteria)
Strain: ATCC 27775 / DSM 1100 / LMG 10767 / O / Gene: Halhy_2296
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F4KU78
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-6X8 / 2-iodanylphenol


Mass: 220.008 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5IO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM Tris-HCl pH 9, 200 mM MgCl2, 2 mM 2-iodophenol, 17% (w/v) PEG 8000, 17% glycerol and 10% (v/v) ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 36524 / % possible obs: 98.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GB5

3gb5


Resolution: 2.103→19.994 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 1821 5 %
Rwork0.1767 --
obs0.179 36430 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.103→19.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 78 126 3418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143395
X-RAY DIFFRACTIONf_angle_d1.3864625
X-RAY DIFFRACTIONf_dihedral_angle_d15.4861249
X-RAY DIFFRACTIONf_chiral_restr0.056495
X-RAY DIFFRACTIONf_plane_restr0.007590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1027-2.15950.35751350.31892544X-RAY DIFFRACTION96
2.1595-2.2230.3371350.292646X-RAY DIFFRACTION100
2.223-2.29460.28651380.25442656X-RAY DIFFRACTION100
2.2946-2.37650.27141330.24182659X-RAY DIFFRACTION100
2.3765-2.47150.27951430.22992663X-RAY DIFFRACTION100
2.4715-2.58380.2781470.22032549X-RAY DIFFRACTION96
2.5838-2.71970.2281350.19992679X-RAY DIFFRACTION100
2.7197-2.88960.24541390.18792691X-RAY DIFFRACTION100
2.8896-3.1120.25421230.18452702X-RAY DIFFRACTION100
3.112-3.42370.20851280.17872623X-RAY DIFFRACTION96
3.4237-3.91590.20431580.15582701X-RAY DIFFRACTION100
3.9159-4.92140.18321540.1442652X-RAY DIFFRACTION96
4.9214-19.99460.20471530.15642844X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -50.0449 Å / Origin y: -31.2175 Å / Origin z: 7.5743 Å
111213212223313233
T0.408 Å20.0049 Å2-0.016 Å2-0.3934 Å20.0054 Å2--0.3807 Å2
L2.5402 °2-0.6032 °20.7445 °2-0.2235 °2-0.1204 °2--0.443 °2
S-0.0943 Å °-0.0504 Å °0.2172 Å °0.027 Å °0.0023 Å °-0.0675 Å °0.0091 Å °0.0963 Å °0.1061 Å °
Refinement TLS groupSelection details: all

+
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