[English] 日本語
Yorodumi
- PDB-7bco: Crystal structure of the sugar acid binding protein DctPAm from A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bco
TitleCrystal structure of the sugar acid binding protein DctPAm from Advenella mimigardefordensis strain DPN7T in complex with D-foconate
ComponentsPutative TRAP transporter solute receptor DctP
KeywordsSUGAR BINDING PROTEIN / sugar acid substrate binding protein TRAP transporter
Function / homologyTRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / (2R,3S,4S,5S)-2,3,4,5-tetrahydroxyhexanoic acid / Putative TRAP transporter solute receptor DctP
Function and homology information
Biological speciesAdvenella mimigardefordensis DPN7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchaefer, L. / Meinert, C. / Kobus, S. / Hoeppner, A. / Smits, S.H. / Steinbuechel, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)417919780 Germany
CitationJournal: Febs J. / Year: 2021
Title: Crystal structure of the sugar acid-binding protein CxaP from a TRAP transporter in Advenella mimigardefordensis strain DPN7 T .
Authors: Schafer, L. / Meinert-Berning, C. / Kobus, S. / Hoppner, A. / Smits, S.H.J. / Steinbuchel, A.
History
DepositionDec 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative TRAP transporter solute receptor DctP
B: Putative TRAP transporter solute receptor DctP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3954
Polymers74,0352
Non-polymers3602
Water6,666370
1
A: Putative TRAP transporter solute receptor DctP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1972
Polymers37,0171
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative TRAP transporter solute receptor DctP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1972
Polymers37,0171
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.166, 92.082, 62.378
Angle α, β, γ (deg.)90.000, 90.007, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Putative TRAP transporter solute receptor DctP / Putative TRAP transporter solute receptor / DctP family


Mass: 37017.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Advenella mimigardefordensis DPN7 (bacteria)
Gene: MIM_c39430 / Production host: Escherichia coli (E. coli) / References: UniProt: R4JTF7
#2: Chemical ChemComp-TF8 / (2R,3S,4S,5S)-2,3,4,5-tetrahydroxyhexanoic acid / (2~{R},3~{S},4~{S},5~{S})-2,3,4,5-tetrakis(oxidanyl)hexanoic acid


Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: PEG4000 / PH range: 7.0-7.4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.967 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2→31.25 Å / Num. obs: 95881 / % possible obs: 92.7 % / Redundancy: 2.3 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 13.57
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 9936

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BBR

7bbr


Resolution: 2→31.25 Å / SU ML: 0.2921 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.0415
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 1987 4.82 %
Rwork0.1997 39218 -
obs0.2032 41205 92.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.05 Å2
Refinement stepCycle: LAST / Resolution: 2→31.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 24 370 5202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01394920
X-RAY DIFFRACTIONf_angle_d1.29136642
X-RAY DIFFRACTIONf_chiral_restr0.0656754
X-RAY DIFFRACTIONf_plane_restr0.0092860
X-RAY DIFFRACTIONf_dihedral_angle_d6.6886648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.3441640.29112903X-RAY DIFFRACTION97.77
2.05-2.110.33851240.25882946X-RAY DIFFRACTION97.31
2.11-2.170.36311570.24342947X-RAY DIFFRACTION97.52
2.17-2.240.34011570.24142931X-RAY DIFFRACTION97.08
2.24-2.320.35891770.25552882X-RAY DIFFRACTION96.47
2.32-2.410.25991630.21432878X-RAY DIFFRACTION96.36
2.41-2.520.2661420.20782865X-RAY DIFFRACTION95.55
2.52-2.650.2841210.19992856X-RAY DIFFRACTION93.88
2.65-2.820.32151140.20292823X-RAY DIFFRACTION92.91
2.82-3.040.28241490.21122682X-RAY DIFFRACTION89.45
3.04-3.340.2739950.20852391X-RAY DIFFRACTION78.7
3.34-3.820.25791350.18342655X-RAY DIFFRACTION87.05
3.82-4.810.25691490.16522751X-RAY DIFFRACTION90.4
4.82-31.250.2311400.18522708X-RAY DIFFRACTION88.06

+
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