[English] 日本語
Yorodumi
- PDB-5jp1: Structure of Xanthomonas campestris effector protein XopD bound t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jp1
TitleStructure of Xanthomonas campestris effector protein XopD bound to tomato SUMO
Components
  • Small ubiquitin-related modifier
  • Xanthomonas outer protein D
KeywordsHYDROLASE / Enzyme / CE clan / Deubiquitinase / DeSUMOylase
Function / homology
Function and homology information


deNEDDylase activity / protein deneddylation / ubiquitin-like protein ligase binding / protein sumoylation / cysteine-type peptidase activity / protein tag activity / proteolysis / nucleus
Similarity search - Function
NEDD8-specific protease 1/2-like / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Papain-like cysteine peptidase superfamily / Ubiquitin homologues ...NEDD8-specific protease 1/2-like / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Papain-like cysteine peptidase superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(4S,5S)-1,2-DITHIANE-4,5-DIOL / MALONATE ION / Xanthomonas outer protein D / Small ubiquitin-related modifier
Similarity search - Component
Biological speciesXanthomonas campestris pv. vesicatoria (bacteria)
Solanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPruneda, J.N. / Komander, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
CitationJournal: Mol.Cell / Year: 2016
Title: The Molecular Basis for Ubiquitin and Ubiquitin-like Specificities in Bacterial Effector Proteases.
Authors: Pruneda, J.N. / Durkin, C.H. / Geurink, P.P. / Ovaa, H. / Santhanam, B. / Holden, D.W. / Komander, D.
History
DepositionMay 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 6, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xanthomonas outer protein D
B: Small ubiquitin-related modifier
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6745
Polymers35,3172
Non-polymers3563
Water3,585199
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint3 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.103, 119.103, 50.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-848-

HOH

21B-212-

HOH

-
Components

#1: Protein Xanthomonas outer protein D


Mass: 24438.215 Da / Num. of mol.: 1 / Fragment: UNP residues 298-515
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. vesicatoria (strain 85-10) (bacteria)
Gene: xopD, XCV0437 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3BYJ5
#2: Protein Small ubiquitin-related modifier / SUMO


Mass: 10879.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: sumo / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SMD1
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M bicine (pH 9.0) 1.6M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.1→59.55 Å / Num. obs: 23605 / % possible obs: 98.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.7
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OIV, 1TGZ

2oiv

1tgz


Resolution: 2.1→59.551 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 1281 5.43 %
Rwork0.1813 --
obs0.1832 23602 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→59.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 22 199 2383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022245
X-RAY DIFFRACTIONf_angle_d0.5073051
X-RAY DIFFRACTIONf_dihedral_angle_d17.5591365
X-RAY DIFFRACTIONf_chiral_restr0.043333
X-RAY DIFFRACTIONf_plane_restr0.004414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.27251220.24782486X-RAY DIFFRACTION99
2.1841-2.28350.2661350.222362X-RAY DIFFRACTION94
2.2835-2.40390.2551320.2112499X-RAY DIFFRACTION99
2.4039-2.55450.25521430.20892482X-RAY DIFFRACTION99
2.5545-2.75180.231590.21172514X-RAY DIFFRACTION99
2.7518-3.02870.25071610.20772444X-RAY DIFFRACTION99
3.0287-3.46690.23281460.17322440X-RAY DIFFRACTION96
3.4669-4.36770.1711580.13362520X-RAY DIFFRACTION100
4.3677-59.57540.17171250.16282574X-RAY DIFFRACTION97
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)
11.5305-0.30840.05461.5009-0.39281.8111-0.00710.12910.177-0.0505-0.00630.069-0.0574-0.05170.01480.13970.013-0.00710.11640.00840.139949.181513.8391-2.147
24.82572.336-1.84123.7374-1.33323.3329-0.0798-0.1746-0.09710.30640.02460.29770.1557-0.2440.06780.2190.01790.03750.1711-0.00230.187742.1295-3.364513.0084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 319 through 514)
2X-RAY DIFFRACTION2(chain 'B' and resid 19 through 96)

+
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