[English] 日本語
Yorodumi
- PDB-6nqz: Flagellar protein FcpB from Leptospira interrogans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nqz
TitleFlagellar protein FcpB from Leptospira interrogans
ComponentsFlagellar coiling protein B
KeywordsPROTEIN FIBRIL / flagellar filament
Function / homologyChem-I3C / IODIDE ION / Uncharacterized protein
Function and homology information
Biological speciesLeptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.58 Å
AuthorsTrajtenberg, F. / Larrieux, N. / Buschiazzo, A.
CitationJournal: Elife / Year: 2020
Title: An asymmetric sheath controls flagellar supercoiling and motility in the Leptospira spirochete.
Authors: Gibson, K. / Trajtenberg, F. / Brady, M. / San Martin, F. / Mechaly, A. / Wunder, E. / Picardeau, M. / Ko, A. / Buschiazzo, A. / Sindelar, C.
History
DepositionJan 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation
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.title / _citation.year
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar coiling protein B
B: Flagellar coiling protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4798
Polymers60,3562
Non-polymers1,1246
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-8 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.735, 65.653, 134.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Flagellar coiling protein B


Mass: 30177.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130) (bacteria)
Strain: Fiocruz L1-130 / Gene: LIC_11848 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72RA0
#2: Chemical ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: (NH4)I, PEG 3350, MES, Glycerol

-
Data collection

DiffractionMean temperature: 109 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.577→67.232 Å / Num. obs: 17479 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 42.84 Å2 / Rpim(I) all: 0.078 / Rrim(I) all: 0.15 / Rsym value: 0.128 / Net I/av σ(I): 5.8 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.58-2.723.60.3951.924420.2410.4640.39597.1
2.72-2.883.60.384223780.2340.4510.38498.8
2.88-3.083.60.2842.722200.1730.3340.28499.2
3.08-3.333.60.1894.120870.1160.2220.18999.5
3.33-3.643.60.126.419360.0740.1410.1299.7
3.64-4.073.60.098.317740.0550.1060.0999.8
4.07-4.73.60.06710.915860.0410.0780.067100
4.7-5.763.50.079.813380.0430.0830.07100
5.76-8.153.40.0828.410840.0510.0970.082100
8.15-37.1513.10.05111.46340.0330.0610.05199.1

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.24data extraction
TRUNCATEdata reduction
SHELXCDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.58→37.01 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.856 / SU R Cruickshank DPI: 0.529 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.539 / SU Rfree Blow DPI: 0.286 / SU Rfree Cruickshank DPI: 0.289
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1029 5.9 %RANDOM
Rwork0.204 ---
obs0.206 17436 99 %-
Displacement parametersBiso max: 122.31 Å2 / Biso mean: 33.32 Å2 / Biso min: 3.06 Å2
Baniso -1Baniso -2Baniso -3
1-4.7442 Å20 Å20 Å2
2---6.3136 Å20 Å2
3---1.5694 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.58→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3410 0 29 31 3470
Biso mean--39.92 21.98 -
Num. residues----423
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1274SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes610HARMONIC5
X-RAY DIFFRACTIONt_it3525HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion454SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3871SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3525HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4752HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion20.83
LS refinement shellResolution: 2.58→2.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2098 20 5.73 %
Rwork0.2552 329 -
all0.2527 349 -
obs--86.28 %

+
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