[English] 日本語
Yorodumi
- PDB-5xhh: crystal structure of Hcp1 from Salmonella typhimurium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xhh
Titlecrystal structure of Hcp1 from Salmonella typhimurium
ComponentsHcp1 family type VI secretion system effector
KeywordsUNKNOWN FUNCTION / effector protein
Function / homologyHcp1-like / : / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Pnp Oxidase; Chain A / Roll / Mainly Beta / Hcp1 family type VI secretion system effector
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLin, Q.P. / Gao, Z.Q. / Zhang, H. / Dong, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
XDB08030103 China
CitationJournal: To Be Published
Title: crystal structure of Hcp1 from Salmonella typhimurium
Authors: Lin, Q.P. / Gao, Z.Q. / Zhang, H. / Dong, Y.H.
History
DepositionApr 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 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: Hcp1 family type VI secretion system effector
B: Hcp1 family type VI secretion system effector
C: Hcp1 family type VI secretion system effector


Theoretical massNumber of molelcules
Total (without water)53,2623
Polymers53,2623
Non-polymers00
Water5,314295
1
A: Hcp1 family type VI secretion system effector


Theoretical massNumber of molelcules
Total (without water)17,7541
Polymers17,7541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hcp1 family type VI secretion system effector


Theoretical massNumber of molelcules
Total (without water)17,7541
Polymers17,7541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hcp1 family type VI secretion system effector


Theoretical massNumber of molelcules
Total (without water)17,7541
Polymers17,7541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.603, 82.771, 142.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Hcp1 family type VI secretion system effector / Putative cytoplasmic protein USSDB7A / SciK protein


Mass: 17753.834 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: sciK, BKC11_01420, BKC12_01390, BLM41_12425, DD95_17690, SEETMRM10961_1345
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H9L4J2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2.2 M Ammonium sulfate, 0.1M ammonium acetate, pH 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28203 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.033 / Net I/σ(I): 27.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1432 / Rpim(I) all: 0.196 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y12

1y12


Resolution: 2.1→41.386 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.36
RfactorNum. reflection% reflection
Rfree0.2398 1416 5.03 %
Rwork0.1922 --
obs0.1945 28145 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3401 0 0 295 3696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083470
X-RAY DIFFRACTIONf_angle_d0.9614685
X-RAY DIFFRACTIONf_dihedral_angle_d16.9582049
X-RAY DIFFRACTIONf_chiral_restr0.061519
X-RAY DIFFRACTIONf_plane_restr0.005594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.17520.28281490.20732558X-RAY DIFFRACTION97
2.1752-2.26230.30511480.22982619X-RAY DIFFRACTION100
2.2623-2.36520.28121600.21342647X-RAY DIFFRACTION100
2.3652-2.48990.27171280.20862652X-RAY DIFFRACTION100
2.4899-2.64590.27771280.20992672X-RAY DIFFRACTION100
2.6459-2.85010.23741330.20682678X-RAY DIFFRACTION100
2.8501-3.13680.25781370.20772669X-RAY DIFFRACTION100
3.1368-3.59050.20581480.1882707X-RAY DIFFRACTION100
3.5905-4.52280.23381450.16782711X-RAY DIFFRACTION100
4.5228-41.39350.21671400.18382816X-RAY DIFFRACTION99

+
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