[English] 日本語
Yorodumi
- PDB-5z7q: Crystal structure of Bacillus cereus flagellin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z7q
TitleCrystal structure of Bacillus cereus flagellin
ComponentsFlagellin
KeywordsIMMUNE SYSTEM / Bacteria / Flagellin / Adjuvant
Function / homology
Function and homology information


bacterial-type flagellum filament / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region
Similarity search - Function
f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal domain / Flagellin, C-terminal domain, subdomain 2 / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKim, M. / Hong, M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National research foundation of korea2015R1D1A1A01057574 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structure of Bacillus cereus flagellin and structure-guided fusion-protein designs
Authors: Il Kim, M. / Lee, C. / Park, J. / Jeon, B.Y. / Hong, M.
History
DepositionJan 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellin


Theoretical massNumber of molelcules
Total (without water)18,7751
Polymers18,7751
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9630 Å2
Unit cell
Length a, b, c (Å)112.724, 112.724, 40.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

-
Components

#1: Protein Flagellin /


Mass: 18774.639 Da / Num. of mol.: 1 / Fragment: UNP residues 54-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_1658 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81FD4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.67 % / Description: rod shape
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M glycine, pH 10, 0.2M lithium sulfate, 1.2M sodium dihydrogen phosphate, and 0.8M di-potassium hydrogen phosphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00002 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 25160 / % possible obs: 99.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Χ2: 2.354 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.885.50.24512390.9650.1150.2711.754100
1.88-1.925.50.22512680.9680.1060.2491.835100
1.92-1.955.50.18712350.9780.0880.2071.995100
1.95-1.995.50.17512670.9820.0820.1932.056100
1.99-2.045.60.15312370.980.0720.1692.274100
2.04-2.085.50.13212430.9840.0620.1462.277100
2.08-2.145.50.12112620.9860.0570.1332.384100
2.14-2.195.60.11312410.9870.0530.1252.425100
2.19-2.265.50.10412840.9890.0490.1152.491100
2.26-2.335.60.09512230.990.0450.1052.447100
2.33-2.415.60.0912650.990.0420.0992.598100
2.41-2.515.60.08412800.9890.040.0932.501100
2.51-2.635.60.07812380.9920.0370.0872.527100
2.63-2.765.50.07112660.9930.0330.0792.536100
2.76-2.945.60.06512680.9950.0310.0722.507100
2.94-3.165.50.05912750.9940.0280.0652.592100
3.16-3.485.50.05312520.9960.0250.0592.477100
3.48-3.995.50.0512970.9950.0240.0562.55599.9
3.99-5.025.40.04612760.9950.0230.0512.39199.2
5.02-504.90.04612440.9960.0230.0522.45293.1

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K8W

3k8w


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.626 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.093 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 1211 4.8 %RANDOM
Rwork0.1863 ---
obs0.1867 23911 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.11 Å2 / Biso mean: 27.198 Å2 / Biso min: 13.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.38 Å2-0 Å2
2---0.77 Å20 Å2
3---2.5 Å2
Refinement stepCycle: final / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 0 153 1447
Biso mean---33.77 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021387
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9611903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9385206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26626.39361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83315254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.087158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021037
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 98 -
Rwork0.189 1738 -
all-1836 -
obs--100 %
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)
16.18982.61290.8021.20620.4550.2474-0.29360.48680.4465-0.1920.21030.2041-0.10880.05990.08330.0758-0.0476-0.06190.06570.07290.117215.669-41.9854.889
25.56982.4779-0.29881.7916-0.18220.7253-0.0704-0.24710.69260.01510.01240.3224-0.0708-0.12040.0580.04220.0161-0.02550.0694-0.01240.17593.767-45.40613.978
37.46124.35621.31053.0030.88340.3105-0.0251-0.1081-0.0397-0.04890.0113-0.1031-0.01440.00370.01380.0259-0.0033-0.00560.04260.0030.05812.992-52.06711.594
42.0285-2.04934.82282.8289-5.291311.69890.2975-0.1021-0.2170.29990.14520.07420.3735-0.2858-0.44270.5320.0274-0.09930.40720.04040.2208-0.659-73.51613.998
53.9096-2.5793-2.7211.78742.667914.5713-0.2262-0.37230.50730.21780.16-0.27580.0954-0.7870.06630.25750.00210.03410.1628-0.07760.1547-15.559-53.54411.987
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A63 - 131
2X-RAY DIFFRACTION2A132 - 179
3X-RAY DIFFRACTION3A180 - 217
4X-RAY DIFFRACTION4A218 - 229
5X-RAY DIFFRACTION5A54 - 62

+
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