[English] 日本語
Yorodumi
- PDB-8ebf: C-terminal (TPR) domain of LIC11990 from Leptospira interrogans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ebf
TitleC-terminal (TPR) domain of LIC11990 from Leptospira interrogans
ComponentsCytoplasmic membrane proteinCell membrane
KeywordsUNKNOWN FUNCTION / tetra-trico-peptide repeats / pathogenesis / virulence / leptospirosis
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
ACETATE ION / Cytoplasmic membrane protein
Similarity search - Component
Biological speciesLeptospira interrogans serovar Copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLarrieux, N. / Buschiazzo, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure and function of a novel membrane-associated protein from Leptospira interrogans (gene LIC11990)
Authors: Wunder, E.A. / Larrieux, N. / Buschiazzo, A.
History
DepositionAug 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytoplasmic membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8776
Polymers82,5161
Non-polymers3615
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.656, 100.093, 170.205
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cytoplasmic membrane protein / Cell membrane


Mass: 82515.867 Da / Num. of mol.: 1 / Fragment: C-terminal (TPR) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni (bacteria)
Gene: LIC_11990 / Plasmid: pQE30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q72QW8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 18% (w/v) PEG 3350, 0.3 M magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97948 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.5→43.68 Å / Num. obs: 29774 / % possible obs: 96.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 76.5 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.09 / Net I/σ(I): 11.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1503 / CC1/2: 0.6 / Rrim(I) all: 1.8 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (8-JUN-2022)refinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→43.68 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.48 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.469 / SU Rfree Blow DPI: 0.292 / SU Rfree Cruickshank DPI: 0.298
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 1465 -RANDOM
Rwork0.2355 ---
obs0.2377 29774 96.5 %-
Displacement parametersBiso mean: 85.5 Å2
Baniso -1Baniso -2Baniso -3
1--30.9669 Å20 Å20 Å2
2--12.1431 Å20 Å2
3---18.8238 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5325 0 24 28 5377
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075463HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.867371HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1912SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes948HARMONIC5
X-RAY DIFFRACTIONt_it5463HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion688SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4353SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion20.16
LS refinement shellResolution: 2.5→2.52 Å
RfactorNum. reflection% reflection
Rfree0.4442 43 -
Rwork0.3917 --
obs0.3955 596 96.41 %
Refinement TLS params.

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)
11.4519-0.22960.27441.27050.3091.7344-0.18790.433-0.07160.4330.1635-0.0395-0.0716-0.03950.02430.7571-0.002-0.03310.33350.05050.45427.237112.974441.5986
20.6483-0.6528-0.27242.27540.212812.052-0.00030.34240.29150.3424-0.2263-0.38990.2915-0.38990.22660.5207-0.1560.05390.6501-0.02730.477426.664320.3766.3797
33.65250.9061.12375.09332.77966.6590.3250.04551.07390.0455-0.0256-0.16241.0739-0.1624-0.29950.585-0.0179-0.00130.4516-0.03980.510132.58069.0239-16.8995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|513 - A|944 }A513 - 944
2X-RAY DIFFRACTION2{ A|945 - A|1045 }A945 - 1045
3X-RAY DIFFRACTION3{ A|1046 - A|1191 }A1046 - 1191

+
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