[English] 日本語
Yorodumi
- PDB-5crb: Crystal Structure of SdeA DUB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5crb
TitleCrystal Structure of SdeA DUB
ComponentsSdeA
KeywordsHYDROLASE / Deubiquitinase / Legionella
Function / homologySidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / NAD+-protein-arginine ADP-ribosyltransferase activity / nucleotide binding / SdeA
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSheedlo, M.J. / Qiu, J. / Luo, Z.Q. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination.
Authors: Sheedlo, M.J. / Qiu, J. / Tan, Y. / Paul, L.N. / Luo, Z.Q. / Das, C.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SdeA
B: SdeA


Theoretical massNumber of molelcules
Total (without water)41,9532
Polymers41,9532
Non-polymers00
Water5,350297
1
A: SdeA


Theoretical massNumber of molelcules
Total (without water)20,9771
Polymers20,9771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SdeA


Theoretical massNumber of molelcules
Total (without water)20,9771
Polymers20,9771
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 area1780 Å2
ΔGint-8 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.410, 76.355, 88.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein SdeA


Mass: 20976.615 Da / Num. of mol.: 2 / Fragment: DUB domain (residues 6-198)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RCR0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M potassium chloride, 0.05 M HEPES:NaOH pH 7.5, 35% (v/v) pentaerythritol/propoxylate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29618 / % possible obs: 97.8 % / Redundancy: 5.8 % / Net I/σ(I): 13.4

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2→36.078 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 24.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 1794 6.76 %
Rwork0.2013 --
obs0.2052 26521 90.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→36.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 0 297 3202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082995
X-RAY DIFFRACTIONf_angle_d1.1124070
X-RAY DIFFRACTIONf_dihedral_angle_d12.1671090
X-RAY DIFFRACTIONf_chiral_restr0.044433
X-RAY DIFFRACTIONf_plane_restr0.006544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.27641350.20311849X-RAY DIFFRACTION89
2.0541-2.11450.3031380.22611920X-RAY DIFFRACTION94
2.1145-2.18280.30371340.22641851X-RAY DIFFRACTION89
2.1828-2.26080.454960.34631283X-RAY DIFFRACTION62
2.2608-2.35130.38831020.27541420X-RAY DIFFRACTION68
2.3513-2.45830.30511430.21431966X-RAY DIFFRACTION95
2.4583-2.58790.26081450.19762002X-RAY DIFFRACTION97
2.5879-2.74990.25241480.20672029X-RAY DIFFRACTION97
2.7499-2.96220.29171480.21852056X-RAY DIFFRACTION98
2.9622-3.26010.26151500.20052081X-RAY DIFFRACTION99
3.2601-3.73140.23191430.18621967X-RAY DIFFRACTION93
3.7314-4.69950.19731510.15662081X-RAY DIFFRACTION97
4.6995-36.08390.2211610.18252222X-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://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