[English] 日本語
Yorodumi
- PDB-7rps: B. miyamotoi FbpB complement inhibitory domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rps
TitleB. miyamotoi FbpB complement inhibitory domain
ComponentsFibronectin-binding lipoprotein FbpB
KeywordsIMMUNE SYSTEM / complement evasion / C1r / Borrelia
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Fibronectin-binding lipoprotein
Function and homology information
Biological speciesBorrelia miyamotoi FR64b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBooth, C.E. / Garcia, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI146930 United States
CitationJournal: Front Immunol / Year: 2022
Title: Borrelia miyamotoi FbpA and FbpB Are Immunomodulatory Outer Surface Lipoproteins With Distinct Structures and Functions.
Authors: Booth Jr., C.E. / Powell-Pierce, A.D. / Skare, J.T. / Garcia, B.L.
History
DepositionAug 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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: Fibronectin-binding lipoprotein FbpB


Theoretical massNumber of molelcules
Total (without water)19,4281
Polymers19,4281
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.724, 46.210, 59.562
Angle α, β, γ (deg.)90.000, 102.943, 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

#1: Protein Fibronectin-binding lipoprotein FbpB


Mass: 19427.795 Da / Num. of mol.: 1 / Fragment: FbpB complement inhibitory domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia miyamotoi FR64b (bacteria) / Gene: BOM_1092, FbpB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W5SFE3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion
Details: 4 mg/mL, 0.2M magnesium chloride, 0.1 tris (8.5), PEG 4000, 0.035 M spermidine

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.975 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 9525 / % possible obs: 96.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 36.18 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.054 / Rrim(I) all: 0.115 / Net I/σ(I): 20.2
Reflection shellResolution: 2.09→2.18 Å / Mean I/σ(I) obs: 2.42 / Num. unique obs: 918 / CC1/2: 0.91 / Rpim(I) all: 0.209 / Rrim(I) all: 0.424 / % possible all: 93.5

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RPR

7rpr


Resolution: 2.09→36.86 Å / SU ML: 0.2011 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.9166
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2563 952 10.01 %
Rwork0.2223 8562 -
obs0.2256 9514 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.2 Å2
Refinement stepCycle: LAST / Resolution: 2.09→36.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 0 36 1288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00981267
X-RAY DIFFRACTIONf_angle_d1.27221701
X-RAY DIFFRACTIONf_chiral_restr0.0589199
X-RAY DIFFRACTIONf_plane_restr0.0054212
X-RAY DIFFRACTIONf_dihedral_angle_d16.6264487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.20.29391250.26561128X-RAY DIFFRACTION89.12
2.2-2.340.26491370.24161226X-RAY DIFFRACTION96.87
2.34-2.520.26171360.24351226X-RAY DIFFRACTION97.56
2.52-2.770.26021410.24251265X-RAY DIFFRACTION98.39
2.78-3.180.27791410.23831261X-RAY DIFFRACTION98.59
3.18-40.25361350.20861219X-RAY DIFFRACTION94.88
4-36.860.23831370.20561237X-RAY DIFFRACTION93.92

+
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