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- PDB-5trg: Structure of Mycobacterium tuberculosis proteasome in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5trg
TitleStructure of Mycobacterium tuberculosis proteasome in complex with N,C-capped dipeptide DPLG-2
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsHYDROLASE/HYDROLASE inhibitor / N / C-capped dipeptides / Mycobacterium tuberculosis / DPLG-2 / proteasome inhibitors / 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 / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / peptidoglycan-based cell wall / proteolysis involved in protein catabolic process / modification-dependent protein catabolic process ...symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / peptidoglycan-based cell wall / proteolysis involved in protein catabolic process / 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 alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-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 alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N,N-diethyl-N~2~-[(2E)-3-phenylprop-2-enoyl]-L-asparaginyl-4-fluoro-N-[(naphthalen-1-yl)methyl]-L-phenylalaninamide / Chem-7HJ / Proteasome subunit alpha / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsHsu, H.-C. / Fan, H. / Singh, R.K. / Wang, R. / Sukenick, G. / Nathan, C. / Lin, G. / 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: Biochemistry / Year: 2017
Title: Structural Basis for the Species-Selective Binding of N,C-Capped Dipeptides to the Mycobacterium tuberculosis Proteasome.
Authors: Hsu, H.C. / Singh, P.K. / Fan, H. / Wang, R. / Sukenick, G. / Nathan, C. / Lin, G. / Li, H.
History
DepositionOct 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Aug 12, 2020Group: Structure summary / Category: pdbx_molecule_features
Revision 1.5Oct 4, 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

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)726,16642
Polymers717,44728
Non-polymers8,71814
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.045, 219.087, 137.894
Angle α, β, γ (deg.)90.00, 104.87, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#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 (bacteria) / Gene: prcA, MRA_2124 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U4D5, UniProt: P9WHU1*PLUS, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / 20S proteasome beta subunit / Proteasome core protein PrcB


Mass: 25274.264 Da / Num. of mol.: 14 / Fragment: UNP residues 58-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcB, MRA_2125 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U4D6, UniProt: P9WHT9*PLUS, proteasome endopeptidase complex
#3: Chemical
ChemComp-7HJ / N,N-diethyl-N~2~-[(2E)-3-phenylprop-2-enoyl]-L-asparaginyl-4-fluoro-N-[(naphthalen-1-yl)methyl]-L-phenylalaninamide


Type: Non-polymer / Class: Inhibitor / Mass: 622.728 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C37H39FN4O4
References: N,N-diethyl-N~2~-[(2E)-3-phenylprop-2-enoyl]-L-asparaginyl-4-fluoro-N-[(naphthalen-1-yl)methyl]-L-phenylalaninamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 60 mM sodium citrate (pH 6.2), 14% PEG-3350,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 167090 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 48.6003639492 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.776 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HFA

3hfa


Resolution: 2.804→49.53 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 8301 4.97 %
Rwork0.1604 --
obs0.1632 167057 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.804→49.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46384 0 644 329 47357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01447743
X-RAY DIFFRACTIONf_angle_d1.29264583
X-RAY DIFFRACTIONf_dihedral_angle_d18.22428443
X-RAY DIFFRACTIONf_chiral_restr0.0737285
X-RAY DIFFRACTIONf_plane_restr0.0098490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8041-2.83590.32482430.24854665X-RAY DIFFRACTION88
2.8359-2.86930.33282740.24055204X-RAY DIFFRACTION98
2.8693-2.90430.34792830.22915220X-RAY DIFFRACTION99
2.9043-2.9410.30192780.21575294X-RAY DIFFRACTION99
2.941-2.97970.2962900.19915294X-RAY DIFFRACTION100
2.9797-3.02050.26262650.19585250X-RAY DIFFRACTION100
3.0205-3.06370.26482830.19455342X-RAY DIFFRACTION100
3.0637-3.10940.26333040.19655232X-RAY DIFFRACTION100
3.1094-3.1580.2552800.19615399X-RAY DIFFRACTION100
3.158-3.20980.26293090.18725232X-RAY DIFFRACTION100
3.2098-3.26510.24832560.18215294X-RAY DIFFRACTION100
3.2651-3.32450.25272820.18485356X-RAY DIFFRACTION100
3.3245-3.38840.24992900.18325273X-RAY DIFFRACTION100
3.3884-3.45750.24092620.17945361X-RAY DIFFRACTION100
3.4575-3.53270.22712810.17135321X-RAY DIFFRACTION100
3.5327-3.61490.22922550.16495297X-RAY DIFFRACTION100
3.6149-3.70520.23752760.16975310X-RAY DIFFRACTION100
3.7052-3.80540.22232830.16015330X-RAY DIFFRACTION100
3.8054-3.91730.20342800.15615313X-RAY DIFFRACTION100
3.9173-4.04370.20932840.15385331X-RAY DIFFRACTION100
4.0437-4.18810.20222630.15665305X-RAY DIFFRACTION100
4.1881-4.35570.2082840.14415324X-RAY DIFFRACTION100
4.3557-4.55380.18212860.13685307X-RAY DIFFRACTION100
4.5538-4.79370.16152820.12945364X-RAY DIFFRACTION100
4.7937-5.09380.17362670.12815330X-RAY DIFFRACTION100
5.0938-5.48660.19482900.13895330X-RAY DIFFRACTION100
5.4866-6.03790.19162690.15195351X-RAY DIFFRACTION100
6.0379-6.90960.21792740.14775347X-RAY DIFFRACTION100
6.9096-8.69770.13242780.11175365X-RAY DIFFRACTION100
8.6977-49.53790.16232500.14675415X-RAY DIFFRACTION99

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