[English] 日本語
Yorodumi
- PDB-7fjr: Structure of a mutant of OspA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fjr
TitleStructure of a mutant of OspA
ComponentsOuter surface protein A
KeywordsLIPOPROTEIN / Outer surface protein A / OspA / LIPID BINDING PROTEIN
Function / homologyOuter surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / membrane / DI(HYDROXYETHYL)ETHER / Outer surface protein A
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsShiga, S. / Makabe, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2024
Title: beta-Strand-mediated Domain-swapping in the Absence of Hydrophobic Core Repacking.
Authors: Kiya, M. / Shiga, S. / Ding, P. / Koide, S. / Makabe, K.
History
DepositionAug 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer surface protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8223
Polymers25,6101
Non-polymers2122
Water1267
1
A: Outer surface protein A
hetero molecules

A: Outer surface protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6446
Polymers51,2192
Non-polymers4244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area2510 Å2
ΔGint2 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.070, 65.070, 309.738
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

#1: Protein Outer surface protein A


Mass: 25609.604 Da / Num. of mol.: 1
Mutation: E37S, E45S, K46S, K48A, K60A, K64S, K83A, E104S, K107S, Deletion 117-119, insertion GG, Deletion 124-127, Deletion 130-133, insertion CTC, K239S, E240S, K254S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Gene: ospA, BB_A15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CL66
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein: 16.0 mg/mL, 35% Polyethylene glycol 400, 0.1 M Tris-HCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→19.69 Å / Num. obs: 12935 / % possible obs: 100 % / Redundancy: 17.7 % / Biso Wilson estimate: 53.83 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 49.3
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 9.2 / Num. unique obs: 1237 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Coot0.8.9.2model building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G8C

2g8c


Resolution: 2.6→19.69 Å / SU ML: 0.2915 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 24.9754
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2965 637 4.96 %
Rwork0.2621 12212 -
obs0.2638 12849 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.91 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 11 7 1770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331770
X-RAY DIFFRACTIONf_angle_d0.53592382
X-RAY DIFFRACTIONf_chiral_restr0.0437304
X-RAY DIFFRACTIONf_plane_restr0.0032296
X-RAY DIFFRACTIONf_dihedral_angle_d17.4802654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80.36411350.322322X-RAY DIFFRACTION100
2.8-3.080.37611150.33592399X-RAY DIFFRACTION100
3.08-3.520.30681170.30452399X-RAY DIFFRACTION100
3.52-4.430.30861310.25152445X-RAY DIFFRACTION100
4.43-19.690.24191390.21822647X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -46.5413778286 Å / Origin y: -16.2906310331 Å / Origin z: 36.3276017197 Å
111213212223313233
T0.482919832547 Å2-0.204274335793 Å2-0.113761490817 Å2-0.539917149259 Å20.117403277141 Å2--0.526508342349 Å2
L0.652030747842 °20.355052227364 °2-0.863783940927 °2-1.32739303232 °2-2.31756804213 °2--4.34561818403 °2
S0.149076924442 Å °0.0916059021778 Å °0.28597372243 Å °0.126098176732 Å °0.0645418591325 Å °0.15110442356 Å °-0.44318709232 Å °0.0376894200765 Å °-0.21017583275 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