[English] 日本語
Yorodumi
- PDB-2ol6: The crystal structure of OspA mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ol6
TitleThe crystal structure of OspA mutant
ComponentsOuter surface protein A
KeywordsMEMBRANE PROTEIN / beta-sheet
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Beta Barrel ...C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Outer surface protein A
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMakabe, K. / Terechko, V. / Koide, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: beta-Strand Flipping and Slipping Triggered by Turn Replacement Reveal the Opportunistic Nature of beta-Strand Pairing
Authors: Makabe, K. / Yan, S. / Tereshko, V. / Gawlak, G. / Koide, S.
History
DepositionJan 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 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
O: Outer surface protein A


Theoretical massNumber of molelcules
Total (without water)26,2511
Polymers26,2511
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.882, 51.508, 65.639
Angle α, β, γ (deg.)90.00, 98.56, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Outer surface protein A


Mass: 26251.213 Da / Num. of mol.: 1 / Fragment: residues 27-273
Mutation: E37S, E45S, K46S, K48A, K60A, K64S, K83A, E104S, K107S, K117N, D118G, K238S, E239S, K253S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: ospA / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q45040
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 32% PEG400, 4% MPD, and 100mM Imidazole, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 28159 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 21.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.96 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G8C

2g8c


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.479 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25877 1427 5.1 %RANDOM
Rwork0.21794 ---
obs0.22005 26475 97.04 %-
all-22172 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.658 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20.47 Å2
2--1.94 Å20 Å2
3----3.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 0 176 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221818
X-RAY DIFFRACTIONr_bond_other_d0.0010.021661
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9842455
X-RAY DIFFRACTIONr_angle_other_deg0.76433926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7275248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6672860
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89815357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.184152
X-RAY DIFFRACTIONr_chiral_restr0.0870.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02289
X-RAY DIFFRACTIONr_nbd_refined0.2050.2269
X-RAY DIFFRACTIONr_nbd_other0.190.21594
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2923
X-RAY DIFFRACTIONr_nbtor_other0.0880.21167
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2138
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2141.51544
X-RAY DIFFRACTIONr_mcbond_other0.2871.5514
X-RAY DIFFRACTIONr_mcangle_it1.49321961
X-RAY DIFFRACTIONr_scbond_it2.7823675
X-RAY DIFFRACTIONr_scangle_it3.9984.5492
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 111 -
Rwork0.305 1922 -
obs--95.45 %

+
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