[English] 日本語
Yorodumi
- PDB-3iqc: Crystal structure of FliS from H. pylori -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iqc
TitleCrystal structure of FliS from H. pylori
ComponentsFlagellar proteinFlagellum
KeywordsCHAPERONE / flagella / Flagellum
Function / homology
Function and homology information


bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / cytosol
Similarity search - Function
Flagellar protein FliS / Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Flagellar secretion chaperone FliS
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLam, W.W.L. / Ling, T.K.W. / Woo, E.J. / Au, S.W.N.
CitationJournal: Faseb J. / Year: 2010
Title: Molecular interaction of flagellar export chaperone FliS and cochaperone HP1076 in Helicobacter pylori
Authors: Lam, W.W.L. / Woo, E.J. / Kotaka, M. / Tam, W.K. / Leung, Y.C. / Ling, T.K.W. / Au, S.W.N.
History
DepositionAug 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 1, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar protein
B: Flagellar protein


Theoretical massNumber of molelcules
Total (without water)29,9402
Polymers29,9402
Non-polymers00
Water19811
1
A: Flagellar protein


Theoretical massNumber of molelcules
Total (without water)14,9701
Polymers14,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar protein


Theoretical massNumber of molelcules
Total (without water)14,9701
Polymers14,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-8 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.469, 92.469, 144.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 5 / Auth seq-ID: 22 - 120 / Label seq-ID: 27 - 125

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Flagellar protein / Flagellum / FliS


Mass: 14969.931 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0753 / Plasmid: pGEX-6p3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: O25448
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.1M Hepes, 0.2M NaCl, 25% PEG3350, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorDate: Aug 28, 2006
RadiationMonochromator: varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→42.68 Å / Num. obs: 8726 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 24.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3 / Num. unique all: 1270 / % possible all: 100

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ORJ

1orj


Resolution: 2.7→30.14 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.949 / SU B: 32.078 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R: 0.516 / ESU R Free: 0.365
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 415 4.8 %RANDOM
Rwork0.2377 ---
obs0.23992 8287 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.863 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 0 11 1787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221800
X-RAY DIFFRACTIONr_bond_other_d0.0010.021198
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.9692432
X-RAY DIFFRACTIONr_angle_other_deg1.10932933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06225.16989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.30415335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5651510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02348
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
589MEDIUM POSITIONAL0.110.5
769LOOSE POSITIONAL0.195
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 29 -
Rwork0.305 625 -
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)
12.94461.5480.70324.65831.61462.92550.0831-0.02270.05970.0896-0.0844-0.2825-0.1330.20910.00130.0165-0.008-0.00650.09060.02620.032337.135-39.87349.831
21.25970.77790.09198.971.8814.00230.09050.12320.3997-0.3393-0.1686-0.0184-0.42590.32040.07810.0628-0.00490.02680.12960.07910.159943.457-22.80737.427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 126
2X-RAY DIFFRACTION2B20 - 120

+
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