[English] 日本語
Yorodumi
- PDB-2qwu: Crystal structure of F. tularensis pathogenicity island protein C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qwu
TitleCrystal structure of F. tularensis pathogenicity island protein C
ComponentsIntracellular growth locus, subunit C
KeywordsCELL INVASION / Francisella tularensis / iglc
Function / homologyIntracellular growth locus C protein / Intracellular growth locus C protein / Intracellular growth locus, subunit C
Function and homology information
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsSun, P. / Austin, B.P. / Schubot, F.D. / Waugh, D.S.
CitationJournal: To be Published
Title: Crystal structure of Francisella tularensis pathogenicity island protein IglC
Authors: Sun, P. / Austin, B.P. / Schubot, F.D. / Waugh, D.S.
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Intracellular growth locus, subunit C
B: Intracellular growth locus, subunit C


Theoretical massNumber of molelcules
Total (without water)45,8302
Polymers45,8302
Non-polymers00
Water7,746430
1
A: Intracellular growth locus, subunit C


Theoretical massNumber of molelcules
Total (without water)22,9151
Polymers22,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intracellular growth locus, subunit C


Theoretical massNumber of molelcules
Total (without water)22,9151
Polymers22,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.031, 83.991, 89.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Intracellular growth locus, subunit C


Mass: 22914.965 Da / Num. of mol.: 2 / Mutation: L36M, L76M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Species: Francisella tularensis / Strain: subsp. tularensis / Gene: iglC2, iglC1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5NEC5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.02 Å3/Da / Density % sol: 39.05 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris-HCl pH 8.5, 27-30% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97939 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2007 / Details: mirror
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.65→35 Å / Num. obs: 78172 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3467 / % possible all: 78.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SGXPROmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→35 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: anomalous data set was used in refinement. THE FRIEDEL PAIRS WERE USED FOR PHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3799 -random
Rwork0.184 ---
obs0.184 78172 90.7 %-
Displacement parametersBiso mean: 27.2532 Å2
Baniso -1Baniso -2Baniso -3
1--8.96 Å20 Å20 Å2
2--4.203 Å20 Å2
3---4.757 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.65→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 0 430 3534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.404
X-RAY DIFFRACTIONc_mcangle_it2.112
LS refinement shellResolution: 1.65→1.71 Å
RfactorNum. reflection% reflection
Rfree0.3365 236 -
Rwork0.2736 --
obs-4638 95.2 %

+
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://pdbjlvh1.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