[English] 日本語
Yorodumi
- PDB-1g5z: CRYSTAL STRUCTURE OF LYME DISEASE ANTIGEN OUTER SURFACE PROTEIN C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g5z
TitleCRYSTAL STRUCTURE OF LYME DISEASE ANTIGEN OUTER SURFACE PROTEIN C (OSPC) FROM BORRELIA BURGDORFERI STRAIN N40
ComponentsOUTER SURFACE PROTEIN C
KeywordsIMMUNE SYSTEM / Surface Protein / Alpha helix protein
Function / homologyLipoprotein, type 6 / Lipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / cell outer membrane / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Outer surface protein C
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsEicken, C. / Sharma, V. / Klabunde, T. / Owens, R.T. / Pikas, D.S. / Hook, M. / Sacchettini, J.C.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of Lyme disease antigen outer surface protein C from Borrelia burgdorferi.
Authors: Eicken, C. / Sharma, V. / Klabunde, T. / Owens, R.T. / Pikas, D.S. / Hook, M. / Sacchettini, J.C.
History
DepositionNov 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 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 C


Theoretical massNumber of molelcules
Total (without water)17,6921
Polymers17,6921
Non-polymers00
Water3,477193
1
A: OUTER SURFACE PROTEIN C

A: OUTER SURFACE PROTEIN C


Theoretical massNumber of molelcules
Total (without water)35,3842
Polymers35,3842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area4150 Å2
ΔGint-34 kcal/mol
Surface area15040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)32.079, 47.052, 110.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

21A-599-

HOH

-
Components

#1: Protein OUTER SURFACE PROTEIN C


Mass: 17692.189 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: O31117
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1500, EDTA, DTT, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
210 mMTris-HCl1reservoir
35 mMdithiothreitol1reservoir
412 %PEG15001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54078 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 23, 1999 / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54078 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 5757 / Num. obs: 5757 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.5 / Redundancy: 3.9 % / Biso Wilson estimate: 31.9 Å2 / Rsym value: 0.067 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.7 % / Rsym value: 0.207 / % possible all: 89.6
Reflection
*PLUS
Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 89.6 % / Rmerge(I) obs: 0.207

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→19.14 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 253477.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 315 5.6 %RANDOM
Rwork0.196 ---
obs0.196 5581 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.83 Å20 Å20 Å2
2---7.58 Å20 Å2
3---0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.51→19.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 0 193 1433
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it1.452
X-RAY DIFFRACTIONc_scangle_it2.172.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 50 6.6 %
Rwork0.251 708 -
obs--75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. reflection obs: 5261 / Rfactor Rfree: 0.262
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66

+
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