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- PDB-2bps: Ubiquitin-like protein YukD of Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2bps
TitleUbiquitin-like protein YukD of Bacillus subtilis
ComponentsYUKD PROTEIN
KeywordsUBIQUITIN / YUKD / UBIQUITIN-LIKE PROTEIN
Function / homologyEsaB / YukD-like / WXG100 protein secretion system (Wss), protein YukD / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta / ESX secretion system protein YukD
Function and homology information
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
Authorsvan den Ent, F. / Lowe, J.
CitationJournal: FEBS Lett. / Year: 2005
Title: Crystal Structure of Ubiquitin-Like Protein Yukd from Bacillus Subtilis
Authors: van den Ent, F. / Lowe, J.
History
DepositionApr 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Source and taxonomy / Category: citation_author / entity_src_gen
Item: _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YUKD PROTEIN
B: YUKD PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4812
Polymers18,4812
Non-polymers00
Water1267
1
A: YUKD PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,2411
Polymers9,2411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: YUKD PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,2411
Polymers9,2411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.328, 50.328, 175.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein YUKD PROTEIN


Mass: 9240.522 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P71071
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.15 Å3/Da / Density % sol: 61 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 6767 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 65.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.7 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→200 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELYHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2963 654 9.7 %RANDOM
Rwork0.241 ---
obs0.241 6703 99.1 %-
Solvent computationBsol: 29.0245 Å2 / ksol: 0.33806 e/Å3
Displacement parametersBiso mean: 53.3 Å2
Baniso -1Baniso -2Baniso -3
1--15.149 Å20 Å20 Å2
2---15.149 Å20 Å2
3---30.297 Å2
Refinement stepCycle: LAST / Resolution: 2.7→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 0 7 1307
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.454 654 10 %
Rwork0.403 451 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER.PARAM

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