[English] 日本語
Yorodumi
- PDB-6iys: Loop deletion and proline insertion mutant (deleting six residues... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6iys
TitleLoop deletion and proline insertion mutant (deleting six residues and inserted three proline residues)
ComponentsOuter surface protein A
KeywordsLIPID BINDING PROTEIN / Outer surface protein A / OspA
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 / Outer surface protein A
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShiga, S. / Makabe, K.
CitationJournal: Chembiochem / Year: 2019
Title: Domain-Swapping Design by Polyproline Rod Insertion.
Authors: Shiga, S. / Yamanaka, M. / Fujiwara, W. / Hirota, S. / Goda, S. / Makabe, K.
History
DepositionDec 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 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


Theoretical massNumber of molelcules
Total (without water)26,1541
Polymers26,1541
Non-polymers00
Water00
1
O: Outer surface protein A

O: Outer surface protein A


Theoretical massNumber of molelcules
Total (without water)52,3092
Polymers52,3092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3480 Å2
ΔGint-31 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.826, 86.826, 105.532
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Outer surface protein A


Mass: 26154.311 Da / Num. of mol.: 1
Mutation: E37S,E45S,K46S,K48A,K60A,K65S,K83A,E104S,K107S,E196A,K239S,E240S,K254S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: ospA, BB_A15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CL66
Sequence detailsDeletion mutant DSSAAT(205-210) to PPP (205-207)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.39 Å3/Da / Density % sol: 71.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7 / Details: 2.5 M Ammonium sulfate 0.1 M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 18350 / % possible obs: 98.3 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 30.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 6.15 / Num. unique obs: 946 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G8C

2g8c


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 23.641 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R: 0.814 / ESU R Free: 0.419 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30031 478 5.1 %RANDOM
Rwork0.24702 ---
obs0.24966 8829 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 111.437 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å21.2 Å20 Å2
2--2.39 Å2-0 Å2
3----7.76 Å2
Refinement stepCycle: 1 / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 0 0 1811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021823
X-RAY DIFFRACTIONr_bond_other_d0.0060.021807
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.9932457
X-RAY DIFFRACTIONr_angle_other_deg1.01734214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9115244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.49127.93158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.83115364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.686152
X-RAY DIFFRACTIONr_chiral_restr0.0850.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022011
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02315
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.84511.034979
X-RAY DIFFRACTIONr_mcbond_other9.82411.029978
X-RAY DIFFRACTIONr_mcangle_it14.69516.5221222
X-RAY DIFFRACTIONr_mcangle_other14.69416.5251223
X-RAY DIFFRACTIONr_scbond_it9.4411.618844
X-RAY DIFFRACTIONr_scbond_other9.4411.618844
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.93817.1261235
X-RAY DIFFRACTIONr_long_range_B_refined21.1997161
X-RAY DIFFRACTIONr_long_range_B_other21.1987162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.076 Å
RfactorNum. reflection% reflection
Rfree0.642 39 -
Rwork0.446 623 -
obs--99.7 %

+
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