[English] 日本語
Yorodumi
- PDB-7ntd: The structure of the SBP TarP_Csal in complex with ferulate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ntd
TitleThe structure of the SBP TarP_Csal in complex with ferulate
ComponentsTRAP dicarboxylate transporter-DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP transporter / solute binding protein / periplasmic / hydroxycinnamate / lignin
Function / homology
Function and homology information


: / transmembrane transport / metal ion binding
Similarity search - Function
TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / TRAP dicarboxylate transporter-DctP subunit
Similarity search - Component
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBisson, C. / Salmon, R.C. / West, L. / Rafferty, J.B. / Hitchcock, A. / Thomas, G.H. / Kelly, D.J.
Funding support1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)
CitationJournal: Febs J. / Year: 2022
Title: The structural basis for high-affinity uptake of lignin-derived aromatic compounds by proteobacterial TRAP transporters.
Authors: Bisson, C. / Salmon, R.C. / West, L. / Rafferty, J.B. / Hitchcock, A. / Thomas, G.H. / Kelly, D.J.
History
DepositionMar 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: TRAP dicarboxylate transporter-DctP subunit
BBB: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1417
Polymers74,6082
Non-polymers5335
Water8,503472
1
AAA: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6184
Polymers37,3041
Non-polymers3153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5223
Polymers37,3041
Non-polymers2182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.860, 52.280, 68.530
Angle α, β, γ (deg.)101.680, 98.590, 104.900
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein TRAP dicarboxylate transporter-DctP subunit


Mass: 37303.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal 6xHis tag and linker
Source: (gene. exp.) Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11) (bacteria)
Strain: ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11
Gene: Csal_0280 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1R0W5
#2: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5 and 20 % (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.75→48.89 Å / Num. obs: 62516 / % possible obs: 96.8 % / Redundancy: 2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.073 / Net I/σ(I): 6.2
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.687 / Num. unique obs: 4572 / CC1/2: 0.47 / Rpim(I) all: 0.62 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NSW

7nsw


Resolution: 1.75→47.124 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.876 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2517 3047 4.875 %
Rwork0.1912 59460 -
all0.194 --
obs-62507 96.822 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.081 Å2
Baniso -1Baniso -2Baniso -3
1--1.778 Å2-0.73 Å20.443 Å2
2--0.895 Å20.543 Å2
3---0.474 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5006 0 35 472 5513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135152
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174759
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.6467001
X-RAY DIFFRACTIONr_angle_other_deg1.3281.57310970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6475640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66522.226283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04515834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3121536
X-RAY DIFFRACTIONr_chiral_restr0.0730.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025890
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021146
X-RAY DIFFRACTIONr_nbd_refined0.1990.21091
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.24539
X-RAY DIFFRACTIONr_nbtor_refined0.160.22467
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2373
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.29
X-RAY DIFFRACTIONr_nbd_other0.1880.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.218
X-RAY DIFFRACTIONr_mcbond_it15.08532566
X-RAY DIFFRACTIONr_mcbond_other15.0692.9992565
X-RAY DIFFRACTIONr_mcangle_it14.3384.4413204
X-RAY DIFFRACTIONr_mcangle_other14.3364.4423205
X-RAY DIFFRACTIONr_scbond_it32.7073.8722586
X-RAY DIFFRACTIONr_scbond_other32.7063.8652581
X-RAY DIFFRACTIONr_scangle_it24.5445.3223797
X-RAY DIFFRACTIONr_scangle_other24.5045.3063792
X-RAY DIFFRACTIONr_lrange_it23.34137.7085890
X-RAY DIFFRACTIONr_lrange_other23.33937.7065891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.3822250.3384340X-RAY DIFFRACTION95.3425
1.795-1.8450.3522400.3114214X-RAY DIFFRACTION95.477
1.845-1.8980.3312220.264071X-RAY DIFFRACTION95.6125
1.898-1.9560.3322260.2324008X-RAY DIFFRACTION96.0526
1.956-2.020.3252040.2373911X-RAY DIFFRACTION96.483
2.02-2.0910.2811860.2073790X-RAY DIFFRACTION96.5986
2.091-2.170.3021520.2053685X-RAY DIFFRACTION96.3102
2.17-2.2580.2811640.1983531X-RAY DIFFRACTION97.0071
2.258-2.3580.2491700.1823385X-RAY DIFFRACTION96.8401
2.358-2.4730.2691810.1793218X-RAY DIFFRACTION97.1698
2.473-2.6070.2591490.1833104X-RAY DIFFRACTION97.3661
2.607-2.7640.2941490.1792932X-RAY DIFFRACTION97.5
2.764-2.9550.2351380.1722747X-RAY DIFFRACTION97.7635
2.955-3.190.2361300.1872546X-RAY DIFFRACTION98.1298
3.19-3.4930.2261130.1942412X-RAY DIFFRACTION98.1345
3.493-3.9030.2221170.1662146X-RAY DIFFRACTION98.3485
3.903-4.5020.197980.1511905X-RAY DIFFRACTION98.67
4.502-5.5020.188810.1591595X-RAY DIFFRACTION98.5303
5.502-7.7330.217610.2021241X-RAY DIFFRACTION97.4551
7.733-47.1240.268410.214679X-RAY DIFFRACTION96.9044

+
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://pdbjlc1.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