[English] 日本語
Yorodumi
- PDB-2vyu: CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vyu
TitleCRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE IN THE PRESENCE OF A PEPTIDOGLYCAN ANALOGUE (TETRASACCHARIDE-PENTAPEPTIDE)
ComponentsCHOLINE BINDING PROTEIN F
KeywordsCHOLINE-BINDING PROTEIN / CBPF / PEPTIDOGLYCAN / CHOLINE-BINDING-PROTEIN / LIPID-BINDING PROTEIN
Function / homology
Function and homology information


left handed beta-beta-3-solenoid - #20 / Cholin Binding / left handed beta-beta-3-solenoid / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
CHOLINE ION / Choline-binding protein F
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsPerez-Dorado, I. / Molina, R. / Hermoso, J.A. / Mobashery, S.
Citation
Journal: Embo Rep. / Year: 2009
Title: Crystal Structure of Cbpf, a Bifunctional Choline-Binding Protein and Autolysis Regulator from Streptococcus Pneumoniae.
Authors: Molina, R. / Gonzalez, A. / Stelter, M. / Perez-Dorado, I. / Kahn, R. / Morales, M. / Campuzano, S. / Campillo, N.E. / Mobashery, S. / Garcia, J.L. / Garcia, P. / Hermoso, J.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Choline-Binding Protein F from Streptococcus Pneumoniae.
Authors: Molina, R. / Gonzalez, A. / Moscoso, M. / Garcia, P. / Stelter, M. / Kahn, R. / Hermoso, J.A.
History
DepositionJul 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 2, 2022Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Jan 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: CHOLINE BINDING PROTEIN F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1138
Polymers39,3841
Non-polymers7297
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.060, 112.730, 79.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein CHOLINE BINDING PROTEIN F


Mass: 39383.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8DR52
#2: Chemical
ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C5H14NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.78 Å3/Da / Density % sol: 55.8 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.953746
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953746 Å / Relative weight: 1
ReflectionResolution: 2.45→45.2 Å / Num. obs: 26724 / % possible obs: 84 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.7
Reflection shellResolution: 2.45→2.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 7.9 / % possible all: 87

-
Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V05

2v05


Resolution: 2.45→41.84 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES FROM 168 TO 178 ARE DISORDERED SO THEY DO NOT APPEAR IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 868 6.8 %RANDOM
Rwork0.198 ---
obs0.198 12713 81.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.79 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2--1.04 Å20 Å2
3---0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.45→41.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 49 277 2818
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 153 7.1 %
Rwork0.208 2017 -
obs--85.6 %

+
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