[English] 日本語
Yorodumi
- PDB-8q4k: Crystal structure of Borrelia burgdorferi BB0158 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q4k
TitleCrystal structure of Borrelia burgdorferi BB0158
ComponentsS2 lipoprotein
KeywordsMEMBRANE PROTEIN / Lyme disease / outer surface protein / borreliosis.
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / S2 lipoprotein
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBrangulis, K. / Tars, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.1/20/A/048European Union
CitationJournal: Ticks Tick Borne Dis / Year: 2024
Title: Structural studies of chromosomally encoded outer surface lipoprotein BB0158 from Borrelia burgdorferi sensu stricto.
Authors: Brangulis, K. / Akopjana, I. / Bogans, J. / Kazaks, A. / Tars, K.
History
DepositionAug 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: S2 lipoprotein
BBB: S2 lipoprotein
CCC: S2 lipoprotein
DDD: S2 lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1237
Polymers96,8354
Non-polymers2883
Water4,468248
1
AAA: S2 lipoprotein
BBB: S2 lipoprotein
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 48.6 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)48,6094
Polymers48,4172
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-77 kcal/mol
Surface area18870 Å2
2
CCC: S2 lipoprotein
DDD: S2 lipoprotein
hetero molecules


  • defined by author
  • 48.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)48,5133
Polymers48,4172
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-49 kcal/mol
Surface area18790 Å2
Unit cell
Length a, b, c (Å)75.063, 81.774, 80.801
Angle α, β, γ (deg.)90.000, 109.381, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
S2 lipoprotein


Mass: 24208.658 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: First 4 residues (GAMG) are remnants from the expression tag after TEV protease cleavage.
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_0158 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51180
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M ammonium sulfate 0.1 M sodium acetate (pH 4.6) 20% PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.4→44.97 Å / Num. obs: 35959 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4 / Num. unique obs: 3725 / CC1/2: 0.938

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.97 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / ESU R: 0.505 / ESU R Free: 0.323
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2973 1821 5.066 %
Rwork0.213 34128 -
all0.217 --
obs-35949 99.255 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.838 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å20 Å20.004 Å2
2---0.003 Å2-0 Å2
3---0.002 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 0 15 248 6736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136603
X-RAY DIFFRACTIONr_bond_other_d0.0340.0166434
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.6378897
X-RAY DIFFRACTIONr_angle_other_deg2.2871.58614959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8185802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93826.545275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.399151301
X-RAY DIFFRACTIONr_chiral_restr0.0650.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027196
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021308
X-RAY DIFFRACTIONr_nbd_refined0.210.21220
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.25933
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23076
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.22895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3430.218
X-RAY DIFFRACTIONr_nbd_other0.3030.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1030.25
X-RAY DIFFRACTIONr_mcbond_it4.1154.9793223
X-RAY DIFFRACTIONr_mcbond_other4.1134.9793222
X-RAY DIFFRACTIONr_mcangle_it6.0447.454020
X-RAY DIFFRACTIONr_mcangle_other6.0447.454021
X-RAY DIFFRACTIONr_scbond_it4.245.3713380
X-RAY DIFFRACTIONr_scbond_other4.2065.3633369
X-RAY DIFFRACTIONr_scangle_it6.4177.8784877
X-RAY DIFFRACTIONr_scangle_other6.4177.8664860
X-RAY DIFFRACTIONr_lrange_it9.11557.4897112
X-RAY DIFFRACTIONr_lrange_other9.10957.477099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.3591430.2752511X-RAY DIFFRACTION99.6246
2.462-2.530.3461330.272415X-RAY DIFFRACTION98.2267
2.53-2.6030.2951210.2322402X-RAY DIFFRACTION99.3698
2.603-2.6830.361370.2622284X-RAY DIFFRACTION99.5068
2.683-2.7710.3951110.2682253X-RAY DIFFRACTION99.5788
2.771-2.8680.3761010.232193X-RAY DIFFRACTION99.2644
2.868-2.9760.3271050.2122086X-RAY DIFFRACTION99.6362
2.976-3.0970.3171040.222039X-RAY DIFFRACTION99.6744
3.097-3.2350.3161070.2241904X-RAY DIFFRACTION98.0976
3.235-3.3920.3181110.2281843X-RAY DIFFRACTION99.4402
3.392-3.5760.3191090.2371771X-RAY DIFFRACTION99.8407
3.576-3.7920.271810.2141667X-RAY DIFFRACTION99.6011
3.792-4.0530.244900.1791583X-RAY DIFFRACTION99.7615
4.053-4.3770.223730.1651458X-RAY DIFFRACTION99.5449
4.377-4.7930.241670.1641344X-RAY DIFFRACTION97.6471
4.793-5.3560.271640.1781236X-RAY DIFFRACTION99.3884
5.356-6.180.325670.2151067X-RAY DIFFRACTION99.561
6.18-7.5560.333350.239949X-RAY DIFFRACTION99.2936
7.556-10.6340.283330.179712X-RAY DIFFRACTION98.545
10.634-44.970.258290.254411X-RAY DIFFRACTION98.2143

+
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