[English] 日本語
Yorodumi
- PDB-4p5p: X-ray structure of Francisella tularensis Rapid Encystment Protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p5p
TitleX-ray structure of Francisella tularensis Rapid Encystment Protein 24 KDa (REP24), gene product of FTN_0841
ComponentsThiJ/PfpI family protein
KeywordsHYDROLASE / cysteine protease / virulence factor / flavodoxin-like
Function / homologyDJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ThiJ/PfpI family protein
Function and homology information
Biological speciesFrancisella tularensis subsp. novicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
AuthorsSegelke, B.W. / Feld, G.K. / Corzett, M.H. / Omattage, N.S. / Rasley, A.
Funding support United States, 2items
OrganizationGrant numberCountry
LDRD09-ERD-054 United States
LDRD12-ERD-031 United States
CitationJournal: To Be Published
Title: X-ray structure of Francisella tularensis Rapid Encystment Protein 24 KDa (REP24), gene product of FTN_0841
Authors: Segelke, B.W. / Feld, G.K. / Corzett, M.H. / Omattage, N.S. / Rasley, A.
History
DepositionMar 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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: ThiJ/PfpI family protein


Theoretical massNumber of molelcules
Total (without water)24,8521
Polymers24,8521
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.439, 44.439, 183.454
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein ThiJ/PfpI family protein / REP24 (Rapid Encystment Protein 24 KDa)


Mass: 24851.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. novicida (bacteria)
Strain: U112 / Gene: FTN_0841 / Plasmid: pETBlueER / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0Q664
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 7.1% (w/v) PEG6000, 0.1M Na-Succinate pH 5.5, 0.58% Heptanoyl-N-methylglucamideMG7
Temp details: room temperature

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.5→61.151 Å / Num. obs: 33819 / % possible obs: 96.9 % / Redundancy: 7 % / Biso Wilson estimate: 16.31 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/av σ(I): 4.91 / Net I/σ(I): 13.4 / Num. measured all: 237816
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym valueNet I/σ(I) obs% possible all
1.5-1.583.20.2262.61296440930.2261.982.9
1.58-1.684.50.21332034845030.2133.595.6
1.68-1.796.90.21433072744700.2146.399.9
1.79-1.949.30.1993.33895741930.19911.7100
1.94-2.128.90.1554.23445038570.15516.7100
2.12-2.378.50.1354.82956334900.13519.9100
2.37-2.7480.1046.22511331340.10422.3100
2.74-3.357.60.0827.62044526820.08223.9100
3.35-4.747.10.0728.71500721190.07224.399.9
4.74-91.6780.0569.81024212780.05626.299.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALA3.2.5data scaling
DENZOdata reduction
Cootmodel building
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U9C

1u9c


Resolution: 1.54→38.486 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 1589 5.01 %Random
Rwork0.1472 30146 --
obs0.1495 31735 98.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.01 Å2 / Biso mean: 20.3215 Å2 / Biso min: 8.32 Å2
Refinement stepCycle: final / Resolution: 1.54→38.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 0 218 1960
Biso mean---29.23 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071846
X-RAY DIFFRACTIONf_angle_d1.1142525
X-RAY DIFFRACTIONf_chiral_restr0.042288
X-RAY DIFFRACTIONf_plane_restr0.005332
X-RAY DIFFRACTIONf_dihedral_angle_d11.73692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.54-1.58970.25781160.16212396251288
1.5897-1.64660.23091400.15252590273095
1.6466-1.71250.20771400.14092711285199
1.7125-1.79040.2171500.136527262876100
1.7904-1.88480.21081620.127527152877100
1.8848-2.00290.21591450.139727622907100
2.0029-2.15750.17731450.135427682913100
2.1575-2.37460.21041310.141627772908100
2.3746-2.71820.21371540.153428222976100
2.7182-3.42430.19421500.157528623012100
3.4243-38.49760.15931560.149730173173100

+
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