[English] 日本語
Yorodumi
- PDB-5ysc: Crystal Structure of periplasmic Vitamin B12 binding protein BtuF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ysc
TitleCrystal Structure of periplasmic Vitamin B12 binding protein BtuF of Vibrio cholerae
ComponentsVitamin B12-binding protein
KeywordsTRANSPORT PROTEIN / Vitamin B12 / ABC trasporter / periplasmic protein / Vibrio cholerae
Function / homology
Function and homology information


cobalamin transport / cobalamin binding / periplasmic space
Similarity search - Function
ABC transporter, vitamin B12-binding protein / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYANOCOBALAMIN / Vitamin B12-binding protein
Similarity search - Component
Biological speciesVibrio cholerae O395 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.673 Å
AuthorsAgarwal, S. / Ghosh, B. / Dasgupta, J.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Mechanistic basis of vitamin B12 and cobinamide salvaging by the Vibrio species.
Authors: Agarwal, S. / Dey, S. / Ghosh, B. / Biswas, M. / Dasgupta, J.
History
DepositionNov 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Aug 25, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Nov 22, 2023Group: 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: Vitamin B12-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0053
Polymers30,5521
Non-polymers1,4522
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-22 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.877, 55.877, 279.163
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Vitamin B12-binding protein


Mass: 30552.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Strain: O395 / Gene: btuF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A5F5P5
#2: Chemical ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C63H89CoN14O14P
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 219 / 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: 1.97 Å3/Da / Density % sol: 37.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.8M ammonium sulfate, 0.1M Tris (pH 8.0) were equilibrated against a 1.6M ammonium sulfate, 0.1M HEPES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.67→47.68 Å / Num. obs: 31146 / % possible obs: 99.5 % / Redundancy: 14.08 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 28.2
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 14.08 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 3.3 / % possible all: 91

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N2Z

1n2z


Resolution: 1.673→47.68 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6
RfactorNum. reflection% reflection
Rfree0.2273 2000 6.45 %
Rwork0.1972 --
obs0.1992 31023 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.673→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 5 219 2349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0632193
X-RAY DIFFRACTIONf_angle_d3.0333028
X-RAY DIFFRACTIONf_dihedral_angle_d20.175799
X-RAY DIFFRACTIONf_chiral_restr0.374328
X-RAY DIFFRACTIONf_plane_restr0.009385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6731-1.7150.2991290.25991875X-RAY DIFFRACTION93
1.715-1.76130.32221400.23612031X-RAY DIFFRACTION100
1.7613-1.81320.26191390.23352021X-RAY DIFFRACTION100
1.8132-1.87170.30771410.23572052X-RAY DIFFRACTION100
1.8717-1.93860.29181400.22172025X-RAY DIFFRACTION100
1.9386-2.01620.22731410.21092041X-RAY DIFFRACTION100
2.0162-2.1080.23841400.22262037X-RAY DIFFRACTION100
2.108-2.21910.24551420.20632059X-RAY DIFFRACTION100
2.2191-2.35810.22771430.20492072X-RAY DIFFRACTION100
2.3581-2.54020.23091440.20332101X-RAY DIFFRACTION100
2.5402-2.79580.24571440.20522091X-RAY DIFFRACTION100
2.7958-3.20030.21691460.1922104X-RAY DIFFRACTION100
3.2003-4.03170.221500.17322178X-RAY DIFFRACTION100
4.0317-47.6990.17671610.17182336X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -25.592 Å / Origin y: 12.228 Å / Origin z: -10.6972 Å
111213212223313233
T0.0894 Å20.0047 Å2-0.0054 Å2-0.0671 Å20.0185 Å2--0.087 Å2
L0.2447 °2-0.2515 °20.1321 °2-0.3697 °2-0.4903 °2--0.4879 °2
S-0.0579 Å °-0.0232 Å °-0.0239 Å °0.1032 Å °-0.0018 Å °-0.0171 Å °-0.0258 Å °0.033 Å °-0.1535 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://pdbjlvh1.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