[English] 日本語
Yorodumi
- PDB-8ec3: The crystal structure of the complement inhibitory domain of Borr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ec3
TitleThe crystal structure of the complement inhibitory domain of Borrelia hermsii FbpC.
ComponentsFibronectin-binding protein
KeywordsIMMUNE SYSTEM / Borrelia hermsii / complement / inhibitor
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Fibronectin-binding protein
Function and homology information
Biological speciesBorrelia hermsii HS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBooth, C.E. / Garcia, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI146930 United States
Citation
Journal: J.Biol.Chem. / Year: 2023
Title: Conformational dynamics of complement protease C1r inhibitor proteins from Lyme disease- and relapsing fever-causing spirochetes.
Authors: Roy, S. / Booth Jr., C.E. / Powell-Pierce, A.D. / Schulz, A.M. / Skare, J.T. / Garcia, B.L.
#1: Journal: Biorxiv / Year: 2023
Title: "Conformational dynamics of C1r inhibitor proteins from Lyme disease and relapsing fever spirochetes".
Authors: Roy, S. / Booth, C.E. / Powell-Pierce, A.D. / Schulz, A.M. / Skare, J.T. / Garcia, B.L.
History
DepositionSep 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9062
Polymers18,8811
Non-polymers241
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.239, 46.557, 45.186
Angle α, β, γ (deg.)90.000, 110.798, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Fibronectin-binding protein


Mass: 18881.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia hermsii HS1 (bacteria) / Gene: cihC, A0V01_04335, BHA007 / Plasmid: pT7HMT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9BXS5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1.99 Å3/Da / Density % sol: 38.2 % / Description: Large birefringent plates
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Crystals were grown in the following condition containing 0.2M magnesium (II) chloride, 0.1M bis-tris (pH 5.5), and 25% PEG 3,350. Crystals were cryoprotected in a buffer containing 0.2M ...Details: Crystals were grown in the following condition containing 0.2M magnesium (II) chloride, 0.1M bis-tris (pH 5.5), and 25% PEG 3,350. Crystals were cryoprotected in a buffer containing 0.2M magnesium (II) chloride, 0.1M sodium citrate (pH 5.4), 25% PEG 3,350, and 10% glycerol.

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→31.28 Å / Num. obs: 23546 / % possible obs: 98.7 % / Redundancy: 7 % / Biso Wilson estimate: 21.7 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rpim(I) all: 0.032 / Rrim(I) all: 0.087 / Net I/σ(I): 19.4
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2109 / CC1/2: 0.87 / CC star: 0.965 / Rpim(I) all: 0.218 / Rrim(I) all: 0.509 / % possible all: 89.2

-
Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.5→31.28 Å / SU ML: 0.1587 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.9463
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1998 1919 8.46 %
Rwork0.1772 20769 -
obs0.1792 22688 95.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.39 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 1 157 1387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011247
X-RAY DIFFRACTIONf_angle_d1.05271667
X-RAY DIFFRACTIONf_chiral_restr0.0532189
X-RAY DIFFRACTIONf_plane_restr0.0076212
X-RAY DIFFRACTIONf_dihedral_angle_d15.7231485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.26651060.26271148X-RAY DIFFRACTION74.07
1.54-1.580.28081170.24631310X-RAY DIFFRACTION85.14
1.58-1.630.23781430.22331418X-RAY DIFFRACTION91.39
1.63-1.680.23451230.21461472X-RAY DIFFRACTION94.32
1.68-1.740.25821260.19591478X-RAY DIFFRACTION95.48
1.74-1.810.26711480.19971509X-RAY DIFFRACTION96.56
1.81-1.890.25131460.19241500X-RAY DIFFRACTION97.45
1.89-1.990.23131360.18711537X-RAY DIFFRACTION98.47
1.99-2.110.21691510.17681541X-RAY DIFFRACTION99.71
2.12-2.280.21351360.1651560X-RAY DIFFRACTION99.71
2.28-2.510.17081530.16341564X-RAY DIFFRACTION99.94
2.51-2.870.18461410.17381558X-RAY DIFFRACTION100
2.87-3.610.17361430.16371581X-RAY DIFFRACTION100
3.62-31.280.19441500.17591593X-RAY DIFFRACTION98.98

+
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://pdbjlvh1.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