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- PDB-5kzf: Crystal structure of near full-length hexameric Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 5kzf
TitleCrystal structure of near full-length hexameric Mycobacterium tuberculosis proteasomal ATPase Mpa in apo form
ComponentsProteasome-associated ATPase
KeywordsHYDROLASE / Proteasome
Function / homology
Function and homology information


proteasomal protein catabolic process / proteasome complex / modification-dependent protein catabolic process / ATP hydrolysis activity / ATP binding
Similarity search - Function
Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities ...Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Proteasome-associated ATPase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsLi, H. / Hu, K. / Yang, S. / Bai, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI070285 United States
CitationJournal: Mol. Microbiol. / Year: 2017
Title: Mycobacterium tuberculosis proteasomal ATPase Mpa has a beta-grasp domain that hinders docking with the proteasome core protease.
Authors: Wu, Y. / Hu, K. / Li, D. / Bai, L. / Yang, S. / Jastrab, J.B. / Xiao, S. / Hu, Y. / Zhang, S. / Darwin, K.H. / Wang, T. / Li, H.
History
DepositionJul 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasome-associated ATPase
B: Proteasome-associated ATPase
C: Proteasome-associated ATPase
D: Proteasome-associated ATPase
E: Proteasome-associated ATPase
F: Proteasome-associated ATPase
G: Proteasome-associated ATPase
H: Proteasome-associated ATPase
I: Proteasome-associated ATPase
J: Proteasome-associated ATPase
K: Proteasome-associated ATPase
L: Proteasome-associated ATPase


Theoretical massNumber of molelcules
Total (without water)682,15312
Polymers682,15312
Non-polymers00
Water00
1
A: Proteasome-associated ATPase
B: Proteasome-associated ATPase
C: Proteasome-associated ATPase
D: Proteasome-associated ATPase
E: Proteasome-associated ATPase
F: Proteasome-associated ATPase


Theoretical massNumber of molelcules
Total (without water)341,0776
Polymers341,0776
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31560 Å2
ΔGint-79 kcal/mol
Surface area122500 Å2
MethodPISA
2
G: Proteasome-associated ATPase
H: Proteasome-associated ATPase
I: Proteasome-associated ATPase
J: Proteasome-associated ATPase
K: Proteasome-associated ATPase
L: Proteasome-associated ATPase


Theoretical massNumber of molelcules
Total (without water)341,0776
Polymers341,0776
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31420 Å2
ΔGint-86 kcal/mol
Surface area124120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.265, 202.590, 303.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Proteasome-associated ATPase / AAA ATPase forming ring-shaped complexes / ARC / Mycobacterial proteasome ATPase


Mass: 56846.094 Da / Num. of mol.: 12 / Fragment: residues 98-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: mpa, MRA_2130 / Production host: Escherichia coli (E. coli) / References: UniProt: A5U4E1

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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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Bis-Tris Propane, pH 7.0, 0.475 M NaCl, 18.2% PEG 4000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.49→71.129 Å / Num. obs: 90439 / % possible obs: 98.7 % / Redundancy: 3.1 % / Net I/σ(I): 9.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.49→71.129 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.872 / Cross valid method: THROUGHOUT / ESU R Free: 0.762 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30564 1996 2.2 %RANDOM
Rwork0.26772 ---
obs0.26856 88443 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 128.92 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å20 Å20 Å2
2--1.19 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 3.49→71.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44299 0 0 0 44299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01945008
X-RAY DIFFRACTIONr_bond_other_d00.0243823
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.98260865
X-RAY DIFFRACTIONr_angle_other_deg3.5553100983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36455633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89624.2262087
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.836158010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.71515374
X-RAY DIFFRACTIONr_chiral_restr0.0530.26959
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02150509
X-RAY DIFFRACTIONr_gen_planes_other0.0020.029509
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1512.86322673
X-RAY DIFFRACTIONr_mcbond_other4.1512.86322672
X-RAY DIFFRACTIONr_mcangle_it6.21219.28428259
X-RAY DIFFRACTIONr_mcangle_other6.21219.28428260
X-RAY DIFFRACTIONr_scbond_it4.13913.0822335
X-RAY DIFFRACTIONr_scbond_other4.13913.0822336
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.01519.53532607
X-RAY DIFFRACTIONr_long_range_B_refined9.23250755
X-RAY DIFFRACTIONr_long_range_B_other9.23150756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.49→3.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 140 -
Rwork0.32 6198 -
obs--95.75 %

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