[English] 日本語
Yorodumi
- PDB-6z34: CymD monoaromatic hydrocarbon channel -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z34
TitleCymD monoaromatic hydrocarbon channel
ComponentsCymD
KeywordsMEMBRANE PROTEIN / FadL monoaromatic hydrocarbons biodegradation toluene outer membrane transport diffusion CymD
Function / homologyOuter membrane protein transport protein (OMPP1/FadL/TodX) / long-chain fatty acid transporting porin activity / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Porin / Beta Barrel / Mainly Beta / membrane / CymD
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
Authorsvan den Berg, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM104495-01 United States
CitationJournal: Nat Commun / Year: 2020
Title: Uptake of monoaromatic hydrocarbons during biodegradation by FadL channel-mediated lateral diffusion.
Authors: Somboon, K. / Doble, A. / Bulmer, D. / Basle, A. / Khalid, S. / van den Berg, B.
History
DepositionMay 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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: CymD


Theoretical massNumber of molelcules
Total (without water)47,2991
Polymers47,2991
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.890, 87.580, 132.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein CymD / Outer membrane protein


Mass: 47298.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Wild type protein, His-tagged / Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: cymD / Production host: Escherichia coli (E. coli) / References: UniProt: O33458
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M bicine/Trizma base pH 8.5, 0.02M mixed monosaccharides, 10-15% PEG 1000/10-15% PEG 3350/12.5% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.27→43.8 Å / Num. obs: 21321 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 52.87 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.031 / Net I/σ(I): 15
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 893 / CC1/2: 0.46 / Rpim(I) all: 0.59 / % possible all: 84.9

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BRZ

3brz


Resolution: 2.27→43.79 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2713 1068 5.01 %
Rwork0.2123 20248 -
obs0.2154 21316 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.15 Å2 / Biso mean: 75.95 Å2 / Biso min: 36.51 Å2
Refinement stepCycle: final / Resolution: 2.27→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 0 13 2899
Biso mean---53.49 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082951
X-RAY DIFFRACTIONf_angle_d1.0734007
X-RAY DIFFRACTIONf_chiral_restr0.058447
X-RAY DIFFRACTIONf_plane_restr0.006517
X-RAY DIFFRACTIONf_dihedral_angle_d7.3881699
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2702-2.37350.42381290.3779227491
2.3735-2.49860.37261020.3101253299
2.4986-2.65510.34231350.252522100
2.6551-2.86010.26211340.2252548100
2.8601-3.14780.2771480.2162538100
3.1478-3.60310.2461340.18392552100
3.6031-4.53880.24561440.18782580100
4.5388-43.790.26941420.20732702100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5197-0.6025-0.79974.42160.08750.2291-0.0551-0.04470.3470.06790.01780.0818-0.4272-0.28040.00660.48510.0807-0.04680.5303-0.05780.468822.8745104.8393132.1609
21.238-0.0294-0.14981.0129-0.4870.6569-0.043-0.04390.0824-0.07910.0007-0.0228-0.51670.01060.04560.46680.1052-0.03630.5238-0.06870.435830.3322104.2849138.9994
31.39690.20411.05380.5090.32842.41130.091-0.3358-0.06790.2629-0.04760.0363-0.0931-0.2109-0.01330.5443-0.07630.00140.5554-0.03320.469128.605998.5739155.2159
42.00820.79250.95880.38180.63851.49110.399-0.3713-0.14680.2834-0.1868-0.04410.0949-0.3091-0.23080.5947-0.01580.00170.4541-0.06670.493925.0951101.2874152.9413
53.3837-0.1619-0.87741.386-0.42723.30140.0681-0.27040.15260.0107-0.11930.1322-0.44960.14940.1090.46550.0882-0.03120.4685-0.04450.608223.7855114.2222135.6244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 42 )A3 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 149 )A43 - 149
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 247 )A150 - 247
4X-RAY DIFFRACTION4chain 'A' and (resid 248 through 346 )A248 - 346
5X-RAY DIFFRACTION5chain 'A' and (resid 347 through 439 )A347 - 439

+
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