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- PDB-5zql: crystal structure of human katanin AAA ATPase domain -

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Basic information

Entry
Database: PDB / ID: 5zql
Titlecrystal structure of human katanin AAA ATPase domain
ComponentsKatanin p60 ATPase-containing subunit A1
KeywordsHYDROLASE / Katanin p60 / AAA ATPase
Function / homology
Function and homology information


katanin complex / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / mitotic spindle pole / cytoplasmic microtubule organization / isomerase activity / spindle pole / spindle / microtubule cytoskeleton ...katanin complex / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / mitotic spindle pole / cytoplasmic microtubule organization / isomerase activity / spindle pole / spindle / microtubule cytoskeleton / midbody / microtubule binding / microtubule / cell cycle / protein heterodimerization activity / cell division / centrosome / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Katanin p60 subunit A1 / Vps4 oligomerisation, C-terminal / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid 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 ...Katanin p60 subunit A1 / Vps4 oligomerisation, C-terminal / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid 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
Katanin p60 ATPase-containing subunit A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.007 Å
AuthorsKim, E.E. / Shin, S.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Korea, Republic Of
CitationJournal: Cell Rep / Year: 2019
Title: Structural and Molecular Basis for Katanin-Mediated Severing of Glutamylated Microtubules.
Authors: Shin, S.C. / Im, S.K. / Jang, E.H. / Jin, K.S. / Hur, E.M. / Kim, E.E.
History
DepositionApr 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
B: Katanin p60 ATPase-containing subunit A1
A: Katanin p60 ATPase-containing subunit A1


Theoretical massNumber of molelcules
Total (without water)70,1302
Polymers70,1302
Non-polymers00
Water0
1
B: Katanin p60 ATPase-containing subunit A1


Theoretical massNumber of molelcules
Total (without water)35,0651
Polymers35,0651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Katanin p60 ATPase-containing subunit A1


Theoretical massNumber of molelcules
Total (without water)35,0651
Polymers35,0651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.810, 97.810, 72.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Katanin p60 ATPase-containing subunit A1 / Katanin p60 subunit A1 / p60 katanin


Mass: 35065.215 Da / Num. of mol.: 2 / Fragment: katanin AAA ATPase domain / Mutation: E309Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KATNA1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75449, EC: 3.6.4.3

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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: 50.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.3 M Lithium citrate acetate pH6.0 20% (v/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 13831 / % possible obs: 94.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.083 / Rrim(I) all: 0.034 / Rsym value: 0.05 / Net I/σ(I): 10.8
Reflection shellResolution: 3→3.05 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 4 / Num. unique obs: 13831 / CC1/2: 0.055 / Rpim(I) all: 0.491 / Rrim(I) all: 0.294 / Rsym value: 0.627 / % possible all: 85.4

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
MOLREPphasing
HKL-2000data scaling
PHENIXphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: SAD
Starting model: 3B9P

3b9p


Resolution: 3.007→37.481 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 33.6
RfactorNum. reflection% reflection
Rfree0.2852 526 4.95 %
Rwork0.2746 --
obs0.2752 10621 76.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.007→37.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4065 0 0 0 4065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054129
X-RAY DIFFRACTIONf_angle_d1.1715549
X-RAY DIFFRACTIONf_dihedral_angle_d17.7371581
X-RAY DIFFRACTIONf_chiral_restr0.045628
X-RAY DIFFRACTIONf_plane_restr0.006698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0065-3.30890.3205440.3028830X-RAY DIFFRACTION25
3.3089-3.78730.34161450.30682776X-RAY DIFFRACTION85
3.7873-4.77010.28961500.26193206X-RAY DIFFRACTION98
4.7701-37.48440.25791870.26623283X-RAY DIFFRACTION99

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