[English] 日本語
Yorodumi
- PDB-2fkg: The Crystal Structure of Engineered OspA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fkg
TitleThe Crystal Structure of Engineered OspA
ComponentsOuter Surface Protein A
KeywordsDE NOVO PROTEIN / BETA SHEET
Function / homology
Function and homology information


cell outer membrane / cell surface / 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 / Outer surface protein A
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMakabe, K. / Terechko, V. / Gawlak, G. / Yan, S. / Koide, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Atomic structures of peptide self-assembly mimics.
Authors: Makabe, K. / McElheny, D. / Tereshko, V. / Hilyard, A. / Gawlak, G. / Yan, S. / Koide, A. / Koide, S.
History
DepositionJan 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)34,9351
Polymers34,9351
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.447, 76.894, 51.941
Angle α, β, γ (deg.)90.00, 120.00, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Outer Surface Protein A


Mass: 34935.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Production host: Escherichia coli (E. coli) / References: UniProt: Q45040, UniProt: P0CL66*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG1000 2% PEG400 0.1M HEPES 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 13450 / Num. obs: 13450 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.26 / Num. unique all: 1339 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 18.977 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.514 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25535 661 5 %RANDOM
Rwork0.21856 ---
all0.2204 13254 --
obs0.2204 12593 99.55 %-
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: 58.776 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å20 Å21.64 Å2
2--2.94 Å20 Å2
3---1.65 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 0 69 2477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222420
X-RAY DIFFRACTIONr_bond_other_d0.0050.022215
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9943234
X-RAY DIFFRACTIONr_angle_other_deg0.83435266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1485314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.38127.69291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.65415529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.486155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02384
X-RAY DIFFRACTIONr_nbd_refined0.2140.2365
X-RAY DIFFRACTIONr_nbd_other0.2110.22021
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21111
X-RAY DIFFRACTIONr_nbtor_other0.0870.21466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.292
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0760.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.26
X-RAY DIFFRACTIONr_mcbond_it1.3931.52025
X-RAY DIFFRACTIONr_mcbond_other0.1211.5654
X-RAY DIFFRACTIONr_mcangle_it1.27222511
X-RAY DIFFRACTIONr_scbond_it2.0043985
X-RAY DIFFRACTIONr_scangle_it3.0164.5723
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 55 -
Rwork0.286 920 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.23650.715-0.60650.8587-0.25142.99260.2211-0.24490.16780.1890.03790.1029-0.2995-0.0339-0.25910.10780.02890.108-0.03140.0397-0.1169-6.93813.953712.7927
25.4627-0.41371.2660.40530.35110.82760.23250.0146-0.0805-0.0996-0.28550.25710.02430.110.0529-0.05620.087-0.0016-0.1220.05420.0451-35.8475-1.6736-3.3919
32.2936-0.77470.42187.41530.38931.39610.32120.3787-0.3589-0.1914-0.130.2116-0.03670.2372-0.1912-0.1310.138-0.0676-0.0453-0.047-0.0649-66.980222.1471-11.9583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA28 - 966 - 74
2X-RAY DIFFRACTION2AA97 - 22575 - 203
3X-RAY DIFFRACTION3AA226 - 342204 - 320

+
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