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- PDB-6mrn: Crystal Structure of ChlaDUB2 DUB domain -

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Basic information

Entry
Database: PDB / ID: 6mrn
TitleCrystal Structure of ChlaDUB2 DUB domain
ComponentsDeubiquitinase and deneddylase Dub2
KeywordsHYDROLASE / Chlamydia / Inclusion / Membrane
Function / homology
Function and homology information


deNEDDylase activity / protein deneddylation / protein deubiquitination / host cell / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region / membrane
Similarity search - Function
Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Deubiquitinase and deneddylase Dub2
Similarity search - Component
Biological speciesChlamydia trachomatis serovar L2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHausman, J.M. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)2R01GM103401 United States
CitationJournal: Biochemistry / Year: 2020
Title: The Two Deubiquitinating Enzymes fromChlamydia trachomatisHave Distinct Ubiquitin Recognition Properties.
Authors: Hausman, J.M. / Kenny, S. / Iyer, S. / Babar, A. / Qiu, J. / Fu, J. / Luo, Z.Q. / Das, C.
History
DepositionOct 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deubiquitinase and deneddylase Dub2


Theoretical massNumber of molelcules
Total (without water)28,5341
Polymers28,5341
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.363, 74.372, 77.407
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Deubiquitinase and deneddylase Dub2 / ChlaDub2


Mass: 28534.320 Da / Num. of mol.: 1 / Fragment: residues 93-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B) (bacteria)
Strain: 434/Bu / ATCC VR-902B / Gene: cdu2, CTL0246 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: B0B999, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES sodium pH 7.5, 2% (v/v) PEG 400, 2M ammonium sulfate, 0.3M NDSB-195

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→53.63 Å / Num. obs: 10827 / % possible obs: 98.72 % / Redundancy: 5.3 % / Biso Wilson estimate: 33.99 Å2 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.107 / Rrim(I) all: 0.2 / Net I/σ(I): 17
Reflection shellResolution: 2.34→2.4 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HAG

5hag


Resolution: 2.29→53.63 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.357 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24725 530 4.9 %RANDOM
Rwork0.1956 ---
obs0.19828 10306 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.496 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å2-0 Å2-0 Å2
2---3.27 Å20 Å2
3---5.74 Å2
Refinement stepCycle: 1 / Resolution: 2.29→53.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 0 32 1943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191951
X-RAY DIFFRACTIONr_bond_other_d0.0020.021783
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9512654
X-RAY DIFFRACTIONr_angle_other_deg1.06734117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7695238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70424.39691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86815321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5541511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2323.95958
X-RAY DIFFRACTIONr_mcbond_other3.2323.948957
X-RAY DIFFRACTIONr_mcangle_it4.9295.9121194
X-RAY DIFFRACTIONr_mcangle_other4.9275.9141195
X-RAY DIFFRACTIONr_scbond_it3.9174.351993
X-RAY DIFFRACTIONr_scbond_other3.9154.352994
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1466.3431461
X-RAY DIFFRACTIONr_long_range_B_refined8.15331.3772172
X-RAY DIFFRACTIONr_long_range_B_other8.15531.3682169
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.292→2.351 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 34 -
Rwork0.29 696 -
obs--92.41 %

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