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- PDB-5ham: Structure of Rickettsia bellii effector protein RickCE -

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Basic information

Entry
Database: PDB / ID: 5ham
TitleStructure of Rickettsia bellii effector protein RickCE
ComponentsRickCE
KeywordsHYDROLASE / Enzyme / CE clan / Deubiquitinase
Function / homology: / RickCE N-terminal / : / RickCE-like, catalytic domain / Papain-like cysteine peptidase superfamily / Ubiquitin-like protease family profile domain-containing protein
Function and homology information
Biological speciesRickettsia bellii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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
DepositionDec 30, 2015Deposition 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 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RickCE
B: RickCE


Theoretical massNumber of molelcules
Total (without water)62,2082
Polymers62,2082
Non-polymers00
Water2,936163
1
A: RickCE


Theoretical massNumber of molelcules
Total (without water)31,1041
Polymers31,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RickCE


Theoretical massNumber of molelcules
Total (without water)31,1041
Polymers31,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.496, 173.496, 55.516
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein RickCE


Mass: 31104.229 Da / Num. of mol.: 2 / Fragment: UNP residues 420-691
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia bellii (bacteria) / Gene: RBE_0198 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RK35
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris (pH 7.5), 2 M Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 2.4→52.08 Å / Num. obs: 24203 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.5
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→52.075 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 1190 4.92 %
Rwork0.1644 --
obs0.167 24197 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→52.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 0 163 4188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084071
X-RAY DIFFRACTIONf_angle_d1.0995497
X-RAY DIFFRACTIONf_dihedral_angle_d15.5591545
X-RAY DIFFRACTIONf_chiral_restr0.07636
X-RAY DIFFRACTIONf_plane_restr0.004724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.50930.32151570.23912893X-RAY DIFFRACTION100
2.5093-2.64160.25851530.22012888X-RAY DIFFRACTION99
2.6416-2.80710.24871540.20492857X-RAY DIFFRACTION100
2.8071-3.02380.26641420.19422838X-RAY DIFFRACTION98
3.0238-3.32810.25771410.17952889X-RAY DIFFRACTION99
3.3281-3.80950.20161630.14152900X-RAY DIFFRACTION100
3.8095-4.79910.17251330.12572895X-RAY DIFFRACTION100
4.7991-52.08730.18161470.15672847X-RAY DIFFRACTION98
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)
11.8309-1.4457-0.8522.44680.81860.91680.0283-0.06330.0709-0.04170.03480.0278-0.02510.0732-0.04870.1917-0.0026-0.04130.1803-0.01740.1467-44.9288-18.0528-9.0411
22.169-0.32940.91861.8983-0.15941.3699-0.1869-0.20090.22910.1604-0.0915-0.11-0.1240.00980.18960.26280.0638-0.01220.2058-0.03640.2032-33.4255-26.2113-5.6443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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