[English] 日本語
Yorodumi
- PDB-6kk9: A Crystal structure of OspA mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kk9
TitleA Crystal structure of OspA mutant
ComponentsOuter Surface Protein A
KeywordsLIPID BINDING PROTEIN / Outer surface protein A
Function / homologyOuter surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Outer Surface Protein A
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShiga, S. / Makabe, K.
CitationJournal: Proteins / Year: 2021
Title: Structural analysis of the beta-sheet edge of peptide self-assembly using a model protein.
Authors: Shiga, S. / Makabe, K.
History
DepositionJul 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
O: Outer Surface Protein A
B: Outer Surface Protein A
C: Outer Surface Protein A
D: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)87,4734
Polymers87,4734
Non-polymers00
Water2,144119
1
O: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)21,8681
Polymers21,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)21,8681
Polymers21,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)21,8681
Polymers21,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)21,8681
Polymers21,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.537, 138.641, 62.514
Angle α, β, γ (deg.)90.000, 100.875, 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
Outer Surface Protein A


Mass: 21868.238 Da / Num. of mol.: 4
Mutation: L103K, L112E, L126K, L135E, L149K, K160Y, L172K, L179V, L181E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0VWU8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 30% PEG 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: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 43410 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 33.1046479172 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.44 / Num. unique obs: 4307 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CKA

3cka


Resolution: 2.2→19.9 Å / SU ML: 0.322766174378 / Cross valid method: FREE R-VALUE / σ(F): 1.33792902289 / Phase error: 31.6423084022
RfactorNum. reflection% reflection
Rfree0.286853310607 2168 5.02235503973 %
Rwork0.222412307257 --
obs0.225655815502 43167 99.53881984 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.1874099348 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5846 0 0 119 5965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009255804650125904
X-RAY DIFFRACTIONf_angle_d1.029192375097898
X-RAY DIFFRACTIONf_chiral_restr0.0594666493116895
X-RAY DIFFRACTIONf_plane_restr0.004839548642351003
X-RAY DIFFRACTIONf_dihedral_angle_d3.234556109573670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25110.3342333804391320.263360583532658X-RAY DIFFRACTION97.1448467967
2.2511-2.30740.3236333924241480.2525285325992722X-RAY DIFFRACTION99.6873914554
2.3074-2.36970.3305370097591340.2455219166312723X-RAY DIFFRACTION99.8252969951
2.3697-2.43930.2784822491451240.2325503960612777X-RAY DIFFRACTION99.9655410062
2.4393-2.51780.3099071819321440.2405939197582749X-RAY DIFFRACTION99.9309153713
2.5178-2.60770.3244344996621320.2471310275112758X-RAY DIFFRACTION99.7928176796
2.6077-2.71180.2952245139971450.2497263076352727X-RAY DIFFRACTION99.9651931779
2.7118-2.83490.3491902766221540.2512456227062716X-RAY DIFFRACTION100
2.8349-2.98390.3214955962081560.2604079927162749X-RAY DIFFRACTION100
2.9839-3.17020.3076034815171310.2545479432662736X-RAY DIFFRACTION100
3.1702-3.41380.3156788691341530.2393572796032744X-RAY DIFFRACTION99.9654934438
3.4138-3.75530.2859782811941660.2069836890052729X-RAY DIFFRACTION99.7587870434
3.7553-4.29390.2584147182781530.1859026611932737X-RAY DIFFRACTION99.9308437068
4.2939-5.39210.2302261351121460.1843483033542730X-RAY DIFFRACTION98.7637362637
5.3921-19.90.2560528693261500.2048318611462744X-RAY DIFFRACTION98.4019041142

+
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