[English] 日本語
Yorodumi
- PDB-7uj2: OspC Type B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uj2
TitleOspC Type B
ComponentsOuter surface protein C
KeywordsUNKNOWN FUNCTION / Outer Surface Protein C Type K
Function / homologyLipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / Outer surface protein C
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.503 Å
AuthorsRudolph, M.J. / Mantis, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Mbio / Year: 2023
Title: Structural Elucidation of a Protective B Cell Epitope on Outer Surface Protein C (OspC) of the Lyme Disease Spirochete, Borreliella burgdorferi.
Authors: Rudolph, M.J. / Davis, S.A. / Haque, H.M.E. / Weis, D.D. / Vance, D.J. / Piazza, C.L. / Ejemel, M. / Cavacini, L. / Wang, Y. / Mbow, M.L. / Gilmore, R.D. / Mantis, N.J.
History
DepositionMar 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer surface protein C
B: Outer surface protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9686
Polymers34,8002
Non-polymers1684
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-61 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.931, 44.085, 68.806
Angle α, β, γ (deg.)90.000, 103.830, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Outer surface protein C


Mass: 17399.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Type K
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Strain: 297 / Gene: ospC / Production host: Escherichia coli (E. coli) / References: UniProt: Q44977
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 1.82 Å3/Da / Density % sol: 32.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM sodium phosphate citrate pH 4.2, 41.9% PEG 600

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 38181 / % possible obs: 95.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.028 / Rrim(I) all: 0.065 / Χ2: 1.034 / Net I/σ(I): 9.1 / Num. measured all: 197208
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.534.60.32519220.9320.1640.3660.44895.6
1.53-1.554.90.30618630.9370.150.3420.48996.5
1.55-1.584.90.27919130.9390.1350.3110.4996.4
1.58-1.6250.26418990.9460.1270.2940.50295.8
1.62-1.655.10.25119190.9540.120.2790.56496.5
1.65-1.695.10.23819020.9280.1140.2650.55596.2
1.69-1.735.20.22818870.970.1080.2530.60996.8
1.73-1.785.10.1919240.9730.0910.2110.63996.1
1.78-1.834.90.16319210.9810.080.1820.71496.8
1.83-1.894.80.14119030.9810.0690.1580.8496.2
1.89-1.964.50.11416930.9850.0570.1280.95584.9
1.96-2.0450.09918420.990.0470.111.02392.1
2.04-2.135.80.08919230.9920.040.0971.16897.5
2.13-2.245.70.07519740.9930.0340.0831.32698.8
2.24-2.385.70.06919800.9950.0320.0761.42898.9
2.38-2.565.60.0619720.9960.0280.0671.43698.9
2.56-2.825.50.05519660.9960.0260.0611.56598.7
2.82-3.235.10.04919640.9960.0240.0551.76797.4
3.23-4.074.80.03917870.9980.0190.0441.89788.2
4.07-505.70.03920270.9980.0180.0431.72797.5

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GGQ

1ggq


Resolution: 1.503→36.797 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 2.09 / Phase error: 15.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1672 1792 4.69 %
Rwork0.1465 36380 -
obs0.1475 38172 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.97 Å2 / Biso mean: 31.5527 Å2 / Biso min: 8.03 Å2
Refinement stepCycle: final / Resolution: 1.503→36.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 13 270 2623
Biso mean--85.58 34.29 -
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122396
X-RAY DIFFRACTIONf_angle_d1.1433208
X-RAY DIFFRACTIONf_chiral_restr0.059397
X-RAY DIFFRACTIONf_plane_restr0.007404
X-RAY DIFFRACTIONf_dihedral_angle_d14.2431528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5033-1.5440.19511340.1754266191
1.544-1.58940.2221340.166281896
1.5894-1.64070.23411380.1611277996
1.6407-1.69930.16871270.1541282497
1.6993-1.76740.19641430.1579281296
1.7674-1.84780.20471480.1535279297
1.8478-1.94520.17711380.1512269092
1.9452-2.06710.14311240.1403265391
2.0671-2.22670.14441280.1314289098
2.2267-2.45070.15861300.1317291799
2.4507-2.80520.16891290.1413292099
2.8052-3.53380.1491760.1475279596
3.5338-36.7970.17041430.1509282993
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)
14.46870.4669-4.44750.1445-0.54095.3248-0.103-0.0681-0.26240.1017-0.07910.0204-0.0847-0.25310.15440.18680.01250.03370.1994-0.00260.1762-22.5073-14.5927-9.5755
21.50280.1872-0.36161.5576-0.80591.7715-0.0151-0.0546-0.1111-0.0009-0.0414-0.00490.1125-0.00460.06880.1077-0.0012-0.01340.0804-0.01760.0982-4.7279-18.1392-22.6899
36.4333-3.8376-6.77832.55643.69367.2318-0.28690.3228-0.68250.1321-0.29650.28660.0125-0.76050.52830.20080.0093-0.02960.2929-0.03420.1563-24.3819-22.366-13.6496
44.17971.1897-4.24140.2638-0.7474.23430.15910.21830.24320.04840.02510.1229-0.1054-0.6373-0.21240.13170.00460.0160.230.00190.1661-23.5942-6.9734-11.8446
52.5233-0.8747-0.97351.75420.42292.05970.02120.0298-0.05830.0685-0.0668-0.00440.0063-0.03850.03040.0946-0.0313-0.00570.0494-0.0070.0719-5.7623-6.6965-22.4969
63.9102-0.2103-4.46581.15680.12855.33820.28560.35670.69990.05430.01820.0481-0.3769-0.4216-0.30690.17080.02830.00570.13340.00940.1853-13.12156.4295-24.0357
75.81150.3187-4.27180.5277-0.4273.50320.1665-0.22040.21070.0994-0.0406-0.0005-0.1802-0.0359-0.17830.1753-0.0076-0.01410.1584-0.03820.1142-12.35571.3754-13.4025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 75 )A40 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 170 )A76 - 170
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 200 )A171 - 200
4X-RAY DIFFRACTION4chain 'B' and (resid 41 through 75 )B41 - 75
5X-RAY DIFFRACTION5chain 'B' and (resid 76 through 120 )B76 - 120
6X-RAY DIFFRACTION6chain 'B' and (resid 121 through 145 )B121 - 145
7X-RAY DIFFRACTION7chain 'B' and (resid 146 through 202 )B146 - 202

+
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