[English] 日本語
Yorodumi
- PDB-3k1i: Crystal strcture of FliS-HP1076 complex in H. pylori -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k1i
TitleCrystal strcture of FliS-HP1076 complex in H. pylori
Components
  • Flagellar proteinFlagellum
  • Putative uncharacterized protein
KeywordsCHAPERONE / Co-chaperone / flagellar system / Helicobacter pylori / Flagellum
Function / homology
Function and homology information


bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / cytosol
Similarity search - Function
Flagellar FLiS export co-chaperone, HP1076 / Flagellar FLiS export co-chaperone, HP1076 / FLiS export co-chaperone, HP1076 superfamily / Flagellar FLiS export co-chaperone, HP1076 / Flagellar protein FliS / Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / Arylsulfatase, C-terminal domain / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Flagellar FLiS export co-chaperone, HP1076 / Flagellar FLiS export co-chaperone, HP1076 / FLiS export co-chaperone, HP1076 superfamily / Flagellar FLiS export co-chaperone, HP1076 / Flagellar protein FliS / Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / Arylsulfatase, C-terminal domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Flagellar secretion chaperone FliS / Uncharacterized protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLam, W.W.L. / Kotaka, M. / Ling, T.K.W. / 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
DepositionSep 28, 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 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
C: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)70,4724
Polymers70,4724
Non-polymers00
Water28816
1
A: Flagellar protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)35,2362
Polymers35,2362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-10 kcal/mol
Surface area12590 Å2
MethodPISA
2
B: Flagellar protein
C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)35,2362
Polymers35,2362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-10 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.253, 50.253, 242.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLUAA19 - 12424 - 129
21SERSERSERSERBB19 - 12224 - 127
12GLNGLNLEULEUCC28 - 14635 - 153
22SERSERLEULEUDD27 - 14634 - 153

NCS ensembles :
ID
1
2

-
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-6p-3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: O25448
#2: Protein Putative uncharacterized protein / HP1076


Mass: 20266.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_1076 / Plasmid: pAC28m / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: O25709
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.1M MES, 0.2M Calcium acetate, 3%(v/v) 2-propanol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2009
Details: Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 17571 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 20.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 2.05 / % possible all: 81.4

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.33 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.873 / SU B: 34.083 / SU ML: 0.322 / Isotropic thermal model: 3IQC, 3K1H / Cross valid method: THROUGHOUT / ESU R: 1.997 / ESU R Free: 0.404
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.29869 771 4.9 %RANDOM
Rwork0.25827 ---
obs0.26024 14883 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.757 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3587 0 0 16 3603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223633
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9854900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8345445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07126.229175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.73615708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1981514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022666
X-RAY DIFFRACTIONr_mcbond_it0.731.52233
X-RAY DIFFRACTIONr_mcangle_it1.38523601
X-RAY DIFFRACTIONr_scbond_it1.69431400
X-RAY DIFFRACTIONr_scangle_it2.7914.51299
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A842tight positional0.10.05
2C934tight positional0.130.05
1A842tight thermal0.240.5
2C934tight thermal0.230.5
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 65 -
Rwork0.336 1120 -
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)
10.51360.46530.22851.13170.62143.5183-0.0364-0.0002-0.0059-0.07720.0438-0.01780.165-0.3211-0.00740.0189-0.02490.00120.0398-0.00070.0003-23.51828.506120.0071
20.6728-0.75990.83181.555-0.69143.5758-0.06390.07360.04090.17420.0539-0.14620.21590.09240.010.04910.0063-0.01910.0343-0.01450.0169-23.34064.8852-3.3086
30.8086-0.12120.48026.7531-1.67232.2967-0.0042-0.13890.01140.14130.03790.1988-0.0466-0.1512-0.03370.00310.00190.0030.0298-0.01050.0288-41.776325.8524-14.5771
44.51080.12191.01551.1652-0.48831.33540.03940.4093-0.1865-0.108-0.0134-0.04530.1230.095-0.02590.02140.00280.01550.0388-0.02190.0397-21.08614.6373-29.2919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 124
2X-RAY DIFFRACTION2B19 - 122
3X-RAY DIFFRACTION3C28 - 146
4X-RAY DIFFRACTION4D27 - 146

+
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