[English] 日本語
Yorodumi
- PDB-7ctq: Peptidyl tryptophan dihydroxylase QhpG essential for tryptophylqu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ctq
TitlePeptidyl tryptophan dihydroxylase QhpG essential for tryptophylquinone cofactor biogenesis
ComponentsPeptidyl tryptophan dihydroxylase
KeywordsFLAVOPROTEIN / FAD-dependent monooxygenase / Cofactor biogenesis / Cysteine tryptophylquinone / Quinohemoprotein amine dehydrogenase
Function / homology
Function and homology information


monooxygenase activity / nucleotide binding
Similarity search - Function
Flavin-dependent halogenase / Tryptophan halogenase / : / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-GKC / HEXANE-1,6-DIOL / FAD-dependent oxidoreductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.978 Å
AuthorsOozeki, T. / Nakai, T. / Okajima, T.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18J22104 Japan
Japan Society for the Promotion of Science (JSPS)JP 23570135 Japan
Japan Society for the Promotion of Science (JSPS)JP 16K07691 Japan
Japan Society for the Promotion of Science (JSPS)JP 24658288 Japan
Japan Society for the Promotion of Science (JSPS)JP 15K07391 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Functional and structural characterization of a flavoprotein monooxygenase essential for biogenesis of tryptophylquinone cofactor.
Authors: Oozeki, T. / Nakai, T. / Kozakai, K. / Okamoto, K. / Kuroda, S. / Kobayashi, K. / Tanizawa, K. / Okajima, T.
History
DepositionAug 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl tryptophan dihydroxylase
B: Peptidyl tryptophan dihydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,34212
Polymers94,5052
Non-polymers2,83710
Water7,584421
1
A: Peptidyl tryptophan dihydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3935
Polymers47,2531
Non-polymers1,1404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-4 kcal/mol
Surface area19600 Å2
MethodPISA
2
B: Peptidyl tryptophan dihydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9497
Polymers47,2531
Non-polymers1,6976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-3 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.610, 51.560, 101.790
Angle α, β, γ (deg.)90.000, 99.770, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Peptidyl tryptophan dihydroxylase


Mass: 47252.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GB LC575123 / Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: NBRC 15366 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A1L5PQA4*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical ChemComp-GKC / (2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{R})-6-(cyclohexylmethoxy)-2-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol


Mass: 438.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H34O11
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsLC575123

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 277.2 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM HEPES (pH 7.0), 20 mM MgCl2, 17% (v/v) Poly(acrylic acid sodium salt) 5100, 1.8% (w/v) 1,6-hexanediol, 34 mM Cyclohexyl-methyl-beta-D-maltoside

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2019
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.978→37.758 Å / Num. obs: 63162 / % possible obs: 98.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 37.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.068 / Net I/σ(I): 12.7
Reflection shellResolution: 1.978→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 19439 / CC1/2: 0.801 / Rrim(I) all: 0.625 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.978→37.758 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 3155 5 %
Rwork0.1817 59987 -
obs0.1837 63142 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.58 Å2 / Biso mean: 45.162 Å2 / Biso min: 16.45 Å2
Refinement stepCycle: final / Resolution: 1.978→37.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6614 0 192 421 7227
Biso mean--50.15 44.71 -
Num. residues----858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.978-2.00720.34841310.2679246995
2.0072-2.03850.29931340.247256598
2.0385-2.07190.26071370.2329260099
2.0719-2.10770.2961340.2307252999
2.1077-2.1460.25081380.2223263499
2.146-2.18730.24391340.209254599
2.1873-2.23190.25131390.2035263499
2.2319-2.28040.23221350.2033257099
2.2804-2.33350.25591380.1975262199
2.3335-2.39180.26131340.1974257099
2.3918-2.45650.25331380.2088261699
2.4565-2.52870.26421360.2061259399
2.5287-2.61030.26541370.2014261499
2.6103-2.70360.25471380.1988262399
2.7036-2.81180.22781360.1927257399
2.8118-2.93970.26361380.1932262999
2.9397-3.09470.24111390.1878263499
3.0947-3.28850.23031380.1941262699
3.2885-3.54220.20321380.1669261999
3.5422-3.89830.19331380.1648263499
3.8983-4.46160.19481410.1552266899
4.4616-5.61820.1951400.15962672100
5.6182-37.7580.18251440.1697274999

+
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