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- PDB-3h6i: Crystal Structure of Mycobacterium Tuberculosis Proteasome Modifi... -

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Basic information

Entry
Database: PDB / ID: 3h6i
TitleCrystal Structure of Mycobacterium Tuberculosis Proteasome Modified by inhibitor GL1
Components
  • Proteasome (Alpha subunit) PrcA
  • Proteasome (Beta subunit) PrcB
KeywordsHYDROLASE / Binding Sites / Oxazolidin-2-one / Mycobacterium tuberculosis / Protease Inhibitors / Proteasome Endopeptidase Complex / Protein Subunits / Substrate Specificity / Proteasome
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / zymogen binding / cell wall / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / peptidoglycan-based cell wall / proteolysis involved in protein catabolic process ...symbiont-mediated perturbation of host defenses / zymogen binding / cell wall / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / 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 / cytosol
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, subunit alpha/beta ...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
DIMETHYLFORMAMIDE / 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: 2.43 Å
AuthorsLi, D. / Li, H. / Lin, G.
CitationJournal: Nature / Year: 2009
Title: Inhibitors selective for mycobacterial versus human proteasomes.
Authors: Lin, G. / Li, D. / de Carvalho, L.P. / Deng, H. / Tao, H. / Vogt, G. / Wu, K. / Schneider, J. / Chidawanyika, T. / Warren, J.D. / Li, H. / Nathan, C.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome (Alpha subunit) PrcA
B: Proteasome (Alpha subunit) PrcA
C: Proteasome (Beta subunit) PrcB
D: Proteasome (Alpha subunit) PrcA
E: Proteasome (Beta subunit) PrcB
F: Proteasome (Alpha subunit) PrcA
G: Proteasome (Beta subunit) PrcB
H: Proteasome (Beta subunit) PrcB
I: Proteasome (Alpha subunit) PrcA
J: Proteasome (Beta subunit) PrcB
K: Proteasome (Alpha subunit) PrcA
L: Proteasome (Beta subunit) PrcB
M: Proteasome (Alpha subunit) PrcA
N: Proteasome (Beta subunit) PrcB
O: Proteasome (Alpha subunit) PrcA
P: Proteasome (Beta subunit) PrcB
Q: Proteasome (Alpha subunit) PrcA
R: Proteasome (Beta subunit) PrcB
S: Proteasome (Alpha subunit) PrcA
T: Proteasome (Beta subunit) PrcB
U: Proteasome (Alpha subunit) PrcA
V: Proteasome (Beta subunit) PrcB
W: Proteasome (Alpha subunit) PrcA
X: Proteasome (Beta subunit) PrcB
Y: Proteasome (Alpha subunit) PrcA
Z: Proteasome (Beta subunit) PrcB
1: Proteasome (Alpha subunit) PrcA
2: Proteasome (Beta subunit) PrcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)738,414130
Polymers730,95828
Non-polymers7,456102
Water42,8942381
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.615, 117.667, 196.335
Angle α, β, γ (deg.)90.00, 113.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Proteasome (Alpha subunit) PrcA


Mass: 26911.039 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcA, Rv2109c / Plasmid: pACYCDuet / Production host: Escherichia coli (E. coli) / Strain (production host): Escherichia coli bl21(de3)
References: UniProt: O33244, UniProt: P9WHU1*PLUS, proteasome endopeptidase complex
#2: Protein
Proteasome (Beta subunit) PrcB / Proteasome / beta subunit


Mass: 25300.258 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2170, prcB, Rv2110c / Plasmid: pACYCDuet / Production host: Escherichia coli (E. coli) / Strain (production host): Escherichia coli bl21(de3)
References: UniProt: O33245, UniProt: P9WHT9*PLUS, proteasome endopeptidase complex
#3: Chemical...
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 102 / Source method: obtained synthetically / Formula: C3H7NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2381 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE HETGROUP OZT IN THE STRUCTURE IS REFERRED TO AS OXZ IN A RELEVANT PUBLICATION.

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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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 277 K / pH: 5.8
Details: 12% PEG 6000, 60 mM sodium citrate, pH 5.8, 0.1M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2008
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→29.75 Å / Num. obs: 261485 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.071 / Net I/σ(I): 14
Reflection shellResolution: 2.43→2.47 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.88 / % possible all: 99.3

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FHG

2fhg


Resolution: 2.43→29.75 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 97069.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME. BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 12991 5 %RANDOM
Rwork0.204 ---
obs0.204 261485 97.8 %-
all-267365 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.6 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.43→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45649 0 510 2381 48540
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.612
X-RAY DIFFRACTIONc_scbond_it2.612
X-RAY DIFFRACTIONc_scangle_it42.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.43→2.52 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.299 1096 4.8 %
Rwork0.271 21637 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_OZT.PARPROTEIN_OZT.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DMF.PARDMF.TOP

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