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- PDB-5tho: Crystal Structure of Mycobacterium Tuberculosis Proteasome in com... -

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Basic information

Entry
Database: PDB / ID: 5tho
TitleCrystal Structure of Mycobacterium Tuberculosis Proteasome in complex with N,C-capped Dipeptide Inhibitor PKS2205
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
Keywordshydrolase/hydrolase inhibitor / Dipeptide Inhibitor / proteasome / Mycobacterium Tuberculosis / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / modification-dependent protein catabolic process / 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~-(3-phenylpropanoyl)-L-asparaginyl-O-methyl-N-[(naphthalen-1-yl)methyl]-L-serinamide / Chem-7C7 / Proteasome subunit alpha / Proteasome subunit beta
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsHsu, H.C. / Li, H.
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
DepositionSep 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Aug 12, 2020Group: Structure summary / Category: pdbx_molecule_features
Revision 1.3Oct 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)725,29742
Polymers717,44728
Non-polymers7,85014
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area84460 Å2
ΔGint-66 kcal/mol
Surface area217140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.163, 198.189, 166.237
Angle α, β, γ (deg.)90.00, 103.35, 90.00
Int Tables number4
Space group name H-MP1211

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: prcA, MRA_2124 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U4D5, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / 20S proteasome beta subunit / Proteasome core protein PrcB


Mass: 25274.264 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: prcB, MRA_2125 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U4D6, proteasome endopeptidase complex
#3: Chemical
ChemComp-7C7 / N,N-diethyl-N~2~-(3-phenylpropanoyl)-L-asparaginyl-O-methyl-N-[(naphthalen-1-yl)methyl]-L-serinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 560.684 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C32H40N4O5
References: N,N-diethyl-N~2~-(3-phenylpropanoyl)-L-asparaginyl-O-methyl-N-[(naphthalen-1-yl)methyl]-L-serinamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 60 mM sodium citrate (pH 6.2) and 14% PEG-3350 / PH range: 5.6-6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→49.55 Å / Num. obs: 146935 / Biso Wilson estimate: 64.7064116616 Å2
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.3 / CC1/2: 0.695 / % possible all: 99.2

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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: 3.002→49.547 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 7272 4.95 %
Rwork0.1765 --
obs0.1782 146935 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.002→49.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46382 0 574 245 47201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00547665
X-RAY DIFFRACTIONf_angle_d0.72564468
X-RAY DIFFRACTIONf_dihedral_angle_d16.67428430
X-RAY DIFFRACTIONf_chiral_restr0.057292
X-RAY DIFFRACTIONf_plane_restr0.0058474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0016-3.03570.31261420.28322804X-RAY DIFFRACTION60
3.0357-3.07150.31892100.27194335X-RAY DIFFRACTION90
3.0715-3.10890.30612160.25544420X-RAY DIFFRACTION93
3.1089-3.14830.31242490.25434594X-RAY DIFFRACTION96
3.1483-3.18970.30332550.25114607X-RAY DIFFRACTION97
3.1897-3.23340.31392210.25374703X-RAY DIFFRACTION97
3.2334-3.27950.32012620.27284560X-RAY DIFFRACTION98
3.2795-3.32850.31052430.24384674X-RAY DIFFRACTION98
3.3285-3.38050.26262360.22534718X-RAY DIFFRACTION99
3.3805-3.43590.25852590.22254741X-RAY DIFFRACTION99
3.4359-3.49510.24972450.20914707X-RAY DIFFRACTION99
3.4951-3.55870.2412570.20054715X-RAY DIFFRACTION99
3.5587-3.62710.22062390.20624792X-RAY DIFFRACTION100
3.6271-3.70110.25542570.20514739X-RAY DIFFRACTION100
3.7011-3.78150.20792350.1934770X-RAY DIFFRACTION100
3.7815-3.86950.22012660.18734740X-RAY DIFFRACTION100
3.8695-3.96620.21412800.17984710X-RAY DIFFRACTION100
3.9662-4.07340.2092340.1764800X-RAY DIFFRACTION100
4.0734-4.19320.21242440.1734777X-RAY DIFFRACTION100
4.1932-4.32850.18322360.16054760X-RAY DIFFRACTION100
4.3285-4.48310.18172590.15414785X-RAY DIFFRACTION100
4.4831-4.66240.18932330.15014791X-RAY DIFFRACTION100
4.6624-4.87450.17062330.14114789X-RAY DIFFRACTION100
4.8745-5.13120.18492390.13994779X-RAY DIFFRACTION100
5.1312-5.45230.18982420.15014819X-RAY DIFFRACTION100
5.4523-5.87270.20192270.164814X-RAY DIFFRACTION100
5.8727-6.46250.19272550.15924785X-RAY DIFFRACTION100
6.4625-7.3950.17792490.14054816X-RAY DIFFRACTION100
7.395-9.30680.12572700.10724812X-RAY DIFFRACTION100
9.3068-49.5540.17412790.1594807X-RAY DIFFRACTION99

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