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- PDB-6ocz: Crystal Structure of Mycobacterium tuberculosis Proteasome in Com... -

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Basic information

Entry
Database: PDB / ID: 6ocz
TitleCrystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-based Inhibitor A86
Components(Proteasome subunit ...) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Mycobacterium tuberculosis / proteasome inhibitor / phenylimidazole / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / modification-dependent protein catabolic process ...symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / modification-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit ...Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / DIMETHYLFORMAMIDE / Chem-M6Y / Proteasome subunit beta / Proteasome subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHsu, H.C. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI070285 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Selective Phenylimidazole-Based Inhibitors of theMycobacterium tuberculosisProteasome.
Authors: Zhan, W. / Hsu, H.C. / Morgan, T. / Ouellette, T. / Burns-Huang, K. / Hara, R. / Wright, A.G. / Imaeda, T. / Okamoto, R. / Sato, K. / Michino, M. / Ramjee, M. / Aso, K. / Meinke, P.T. / ...Authors: Zhan, W. / Hsu, H.C. / Morgan, T. / Ouellette, T. / Burns-Huang, K. / Hara, R. / Wright, A.G. / Imaeda, T. / Okamoto, R. / Sato, K. / Michino, M. / Ramjee, M. / Aso, K. / Meinke, P.T. / Foley, M. / Nathan, C.F. / Li, H. / Lin, G.
History
DepositionMar 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit beta
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
O: Proteasome subunit alpha
P: Proteasome subunit alpha
Q: Proteasome subunit alpha
R: Proteasome subunit alpha
S: Proteasome subunit alpha
T: Proteasome subunit alpha
U: Proteasome subunit alpha
V: Proteasome subunit beta
W: Proteasome subunit beta
X: Proteasome subunit beta
Y: Proteasome subunit beta
Z: Proteasome subunit beta
a: Proteasome subunit beta
b: Proteasome subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)717,94176
Polymers705,84328
Non-polymers12,09848
Water15,385854
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area95080 Å2
ΔGint5 kcal/mol
Surface area217930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.768, 198.062, 167.919
Angle α, β, γ (deg.)90.000, 103.720, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Proteasome subunit ... , 2 types, 28 molecules ABCDEFGOPQRSTUHIJKLMNVWXYZab

#1: Protein
Proteasome subunit alpha / 20S proteasome alpha subunit / Proteasome core protein PrcA


Mass: 25971.975 Da / Num. of mol.: 14 / Fragment: UNP residues 10-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: prcA, Rv2109c / Production host: Escherichia coli (E. coli)
References: UniProt: P9WHU1, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / 20S proteasome beta subunit / Proteasome core protein PrcB


Mass: 24445.383 Da / Num. of mol.: 14 / Fragment: UNP residues 58-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: prcB, Rv2110c / Production host: Escherichia coli (E. coli)
References: UniProt: P9WHT9, proteasome endopeptidase complex

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Non-polymers , 4 types, 902 molecules

#3: Chemical
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H7NO
#4: Chemical
ChemComp-M6Y / N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-1,4-dioxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide (non-preferred name)


Type: peptide-like / Mass: 567.584 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C29H31F2N5O5
#5: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / 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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 60 mM sodium citrate, pH 6.2, 14% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 15, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.65→44.63 Å / Num. obs: 207497 / % possible obs: 93.8 % / Redundancy: 3.5 % / CC1/2: 0.983 / Rmerge(I) obs: 0.141 / Net I/σ(I): 6.7
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 29158 / CC1/2: 0.686 / % possible all: 90.4

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→42.919 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2355 10226 4.93 %
Rwork0.1841 --
obs0.1867 207317 93.49 %
Displacement parametersBiso mean: 34.75 Å2
Refinement stepCycle: LAST / Resolution: 2.65→42.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46315 0 856 854 48025

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