[English] 日本語
Yorodumi
- PDB-5kc0: Crystal structure of TmRibU, hexagonal crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kc0
TitleCrystal structure of TmRibU, hexagonal crystal form
ComponentsRiboflavin transporter RibU
KeywordsTransport Protein/Membrane Protein / membrane transport / integral membrane protein / vitamins / thermophile / Transport Protein-Membrane Protein complex
Function / homology
Function and homology information


riboflavin transport / riboflavin transmembrane transporter activity / plasma membrane
Similarity search - Function
ECF transporter, Riboflavin transporter RibU / ECF transporter, substrate-specific component / ECF transporter, substrate-specific component / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RIBOFLAVIN / Riboflavin transporter RibU
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2001 Å
AuthorsKarpowich, N.K. / Wang, D.N. / Song, J.M.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin.
Authors: Karpowich, N.K. / Song, J. / Wang, D.N.
History
DepositionJun 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Riboflavin transporter RibU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7754
Polymers20,7861
Non-polymers9893
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint1 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.611, 72.611, 232.912
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsMonomer confirmed by Analytical SEC

-
Components

#1: Protein Riboflavin transporter RibU / Riboflavin ECF transporter S component RibU


Mass: 20785.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: ribU, TM_1455 / Plasmid: pBADCtmycHis / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X1G6
#2: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.42 Å3/Da / Density % sol: 72.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium acetate, pH 4.5, 28% PEG400, and 50 mM magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→37.431 Å / Num. obs: 6009 / % possible obs: 91.2 % / Observed criterion σ(F): 2 / Redundancy: 18.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 31.3
Reflection shellResolution: 3.2→3.28 Å / Rmerge(I) obs: 0.062

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P5N

3p5n


Resolution: 3.2001→37.4 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 32.45
RfactorNum. reflection% reflection
Rfree0.2983 301 5.01 %
Rwork0.2663 --
obs0.2681 6009 91.28 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Refinement stepCycle: LAST / Resolution: 3.2001→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 69 0 1347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031387
X-RAY DIFFRACTIONf_angle_d0.6391875
X-RAY DIFFRACTIONf_dihedral_angle_d12.305779
X-RAY DIFFRACTIONf_chiral_restr0.037225
X-RAY DIFFRACTIONf_plane_restr0.006217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-4.0310.28621340.28652541X-RAY DIFFRACTION84
4.031-37.43350.30251670.25993167X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 27.4819 Å / Origin y: 11.8601 Å / Origin z: 125.5656 Å
111213212223313233
T0.6897 Å2-0.1944 Å20.0395 Å2-0.6202 Å2-0.0009 Å2--0.6305 Å2
L0.6812 °2-0.261 °20.251 °2-1.4289 °20.8362 °2--0.7406 °2
S0.2788 Å °-0.3748 Å °0.2047 Å °0.0736 Å °-0.2977 Å °-0.0754 Å °-0.2609 Å °0.1451 Å °0.0513 Å °
Refinement TLS groupSelection details: all

+
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