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- PDB-3mi0: Crystal Structure of Mycobacterium Tuberculosis Proteasome at 2.2 A -

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Basic information

Entry
Database: PDB / ID: 3mi0
TitleCrystal Structure of Mycobacterium Tuberculosis Proteasome at 2.2 A
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsHYDROLASE / Enzyme Inhibitors / Lactones / Proteasome Endopeptidase Complex / Mycobacterium tuberculosis
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 / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / proteasomal 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 / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / proteasomal protein catabolic process / modification-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, 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 / Chem-SA6 / 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: 2.2 Å
AuthorsLi, D. / Li, H.
CitationJournal: Embo J. / Year: 2010
Title: Structural basis for the assembly and gate closure mechanisms of the Mycobacterium tuberculosis 20S proteasome.
Authors: Li, D. / Li, H. / Wang, T. / Pan, H. / Lin, G. / Li, H.
History
DepositionApr 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 beta
D: Proteasome subunit alpha
E: Proteasome subunit beta
F: Proteasome subunit alpha
G: Proteasome subunit beta
H: Proteasome subunit beta
I: Proteasome subunit alpha
J: Proteasome subunit beta
K: Proteasome subunit alpha
L: Proteasome subunit beta
M: Proteasome subunit alpha
N: Proteasome subunit beta
O: Proteasome subunit alpha
P: Proteasome subunit beta
Q: Proteasome subunit alpha
R: Proteasome subunit beta
S: Proteasome subunit alpha
T: Proteasome subunit beta
U: Proteasome subunit alpha
V: Proteasome subunit beta
W: Proteasome subunit alpha
X: Proteasome subunit beta
Y: Proteasome subunit alpha
Z: Proteasome subunit beta
1: Proteasome subunit alpha
2: Proteasome subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)743,524165
Polymers730,59428
Non-polymers12,929137
Water48,2802680
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.374, 118.436, 195.249
Angle α, β, γ (deg.)90.00, 113.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 26911.039 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: rv2109c / Gene: MT2169, prcA, Rv2109c / Plasmid: pACYCDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O33244, UniProt: P9WHU1*PLUS, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / / Proteasome core protein prcB / 20S proteasome beta subunit


Mass: 25274.264 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: rv2109c / Gene: MT2170, prcB, Rv2110c / Plasmid: pACYCDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O33245, UniProt: P9WHT9*PLUS, proteasome endopeptidase complex
#3: Chemical...
ChemComp-DMF / DIMETHYLFORMAMIDE / Dimethylformamide


Mass: 73.094 Da / Num. of mol.: 123 / Source method: obtained synthetically / Formula: C3H7NO
#4: Chemical
ChemComp-SA6 / (2R,3S,4R)-2-[(S)-(1S)-cyclohex-2-en-1-yl(hydroxy)methyl]-4-ethyl-3-hydroxy-3-methyl-5-oxopyrrolidine-2-carbaldehyde


Mass: 281.347 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C15H23NO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2680 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 13.2% PEG 6000, 60mM sodium citrate, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 28, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 378907 / Num. obs: 362039 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 1.4 / Num. unique all: 33082 / % possible all: 82.7

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Processing

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

2fhg


Resolution: 2.2→24.95 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 96363.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.234 16559 5 %RANDOM
Rwork0.205 ---
all0.225 361323 --
obs0.205 332584 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.3711 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å20.27 Å2
2---2.97 Å20 Å2
3---0.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46505 0 895 2680 50080
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.34
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
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.31 1384 4.9 %
Rwork0.295 26599 -
obs-27983 77.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4DMF.paramDMF.top
X-RAY DIFFRACTION5SA6.paramSA6.top

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