[English] 日本語
Yorodumi
- PDB-7ndr: Crystal structure of TphC in an open conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ndr
TitleCrystal structure of TphC in an open conformation
ComponentsTripartite tricarboxylate transporter substrate binding protein
KeywordsTRANSPORT PROTEIN / Solute binding protein
Function / homologyBordetella uptake gene / Bordetella uptake gene, domain 1 / Tripartite tricarboxylate transporter family receptor / Tripartite tricarboxylate transporter substrate binding protein
Function and homology information
Biological speciesComamonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsLevy, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Commonwealth Scholarship Commission (United Kingdom)INCN-2018-57 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of terephthalate recognition by solute binding protein TphC.
Authors: Gautom, T. / Dheeman, D. / Levy, C. / Butterfield, T. / Alvarez Gonzalez, G. / Le Roy, P. / Caiger, L. / Fisher, K. / Johannissen, L. / Dixon, N.
History
DepositionFeb 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _audit_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tripartite tricarboxylate transporter substrate binding protein
B: Tripartite tricarboxylate transporter substrate binding protein
C: Tripartite tricarboxylate transporter substrate binding protein
D: Tripartite tricarboxylate transporter substrate binding protein
E: Tripartite tricarboxylate transporter substrate binding protein
F: Tripartite tricarboxylate transporter substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,8808
Polymers202,7566
Non-polymers1242
Water29,7071649
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint0 kcal/mol
Surface area69790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.113, 81.269, 186.953
Angle α, β, γ (deg.)90.000, 109.547, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-496-

HOH

21B-598-

HOH

31C-423-

HOH

41C-652-

HOH

-
Components

#1: Protein
Tripartite tricarboxylate transporter substrate binding protein


Mass: 33792.711 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas sp. (bacteria) / Gene: E2578_22390 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5N7XFM8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1649 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus B5 - 0.09M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide) 0.1M Buffer System 2 pH 7.5 (1.0M 7.5 Sodium HEPES; MOPS (acid) ) 30% v/v precipitant mix 1 (40% ...Details: Morpheus B5 - 0.09M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide) 0.1M Buffer System 2 pH 7.5 (1.0M 7.5 Sodium HEPES; MOPS (acid) ) 30% v/v precipitant mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)
Temp details: Cold room

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.88→70.48 Å / Num. obs: 161975 / % possible obs: 99.41 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.13 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.2251 / Rpim(I) all: 0.0927 / Rrim(I) all: 0.2438 / Net I/σ(I): 6.9
Reflection shellResolution: 1.88→1.947 Å / Redundancy: 7.1 % / Rmerge(I) obs: 2.175 / Mean I/σ(I) obs: 0.56 / Num. unique obs: 16108 / CC1/2: 0.838 / CC star: 0.955 / Rpim(I) all: 0.88 / Rrim(I) all: 2.35 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X9T

4x9t


Resolution: 1.97→70.48 Å / SU ML: 0.2274 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5947
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2215 7252 5.15 %
Rwork0.1822 133470 -
obs0.1842 140722 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.21 Å2
Refinement stepCycle: LAST / Resolution: 1.97→70.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13259 0 8 1649 14916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013113643
X-RAY DIFFRACTIONf_angle_d0.894618624
X-RAY DIFFRACTIONf_chiral_restr0.06312163
X-RAY DIFFRACTIONf_plane_restr0.012423
X-RAY DIFFRACTIONf_dihedral_angle_d13.14744998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-1.990.29812230.28454452X-RAY DIFFRACTION99.6
1.99-2.020.32362270.27954410X-RAY DIFFRACTION99.63
2.02-2.040.31992400.26194462X-RAY DIFFRACTION99.87
2.04-2.070.27752480.26754300X-RAY DIFFRACTION99.8
2.07-2.090.31292490.25484478X-RAY DIFFRACTION99.77
2.09-2.120.26262390.23664401X-RAY DIFFRACTION99.94
2.12-2.150.27082270.23374464X-RAY DIFFRACTION99.98
2.15-2.180.27182430.23024397X-RAY DIFFRACTION99.94
2.18-2.220.27082590.22594433X-RAY DIFFRACTION99.94
2.22-2.260.27512630.22984426X-RAY DIFFRACTION99.83
2.26-2.290.27932780.22474380X-RAY DIFFRACTION99.94
2.29-2.340.25312500.20994402X-RAY DIFFRACTION99.91
2.34-2.380.24082460.20094478X-RAY DIFFRACTION99.89
2.38-2.430.23062230.1864393X-RAY DIFFRACTION99.68
2.43-2.480.24672080.18394488X-RAY DIFFRACTION99.96
2.48-2.540.25162360.18474486X-RAY DIFFRACTION99.98
2.54-2.60.22612400.18474423X-RAY DIFFRACTION99.96
2.6-2.670.2362770.17914366X-RAY DIFFRACTION100
2.67-2.750.23822330.1764483X-RAY DIFFRACTION99.96
2.75-2.840.21432390.17774434X-RAY DIFFRACTION99.98
2.84-2.940.22282250.17674469X-RAY DIFFRACTION99.91
2.94-3.060.2252330.18584480X-RAY DIFFRACTION99.98
3.06-3.20.22932410.18144438X-RAY DIFFRACTION99.96
3.2-3.370.20032160.17914513X-RAY DIFFRACTION100
3.37-3.580.21562320.16844472X-RAY DIFFRACTION99.96
3.58-3.860.18832330.16254504X-RAY DIFFRACTION100
3.86-4.240.16532600.1414448X-RAY DIFFRACTION99.96
4.24-4.860.15372500.12094495X-RAY DIFFRACTION99.92
4.86-6.120.18442600.15034510X-RAY DIFFRACTION99.96
6.12-70.480.22342540.18144585X-RAY DIFFRACTION99.32

+
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