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- PDB-5zqm: Crystal structure of human katanin AAA ATPase domain complex with... -

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Basic information

Entry
Database: PDB / ID: 5zqm
TitleCrystal structure of human katanin AAA ATPase domain complex with ATPgammaS
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 / spindle / spindle pole / microtubule cytoskeleton / midbody ...katanin complex / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / mitotic spindle pole / cytoplasmic microtubule organization / spindle / spindle pole / microtubule cytoskeleton / midbody / microtubule binding / microtubule / protein heterodimerization activity / cell division / centrosome / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
: / : / Katanin p60 subunit A1, MIT domain / 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 ...: / : / Katanin p60 subunit A1, MIT domain / 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 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Katanin p60 ATPase-containing subunit A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.1Nov 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
A: Katanin p60 ATPase-containing subunit A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5412
Polymers35,0181
Non-polymers5231
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-4 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.907, 68.907, 138.698
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 35018.141 Da / Num. of mol.: 1 / Fragment: katanin AAA ATPase domain
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
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.4 M Calcium acetate 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 8212 / % possible obs: 98.5 % / Redundancy: 7.8 % / Biso Wilson estimate: 61.08 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.036 / Rrim(I) all: 0.115 / Χ2: 1.492 / Net I/σ(I): 11 / Num. measured all: 64181
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-33.10.3867680.0830.2310.4540.62391.5
3-3.124.20.3677920.3550.1920.4170.69497.2
3.12-3.275.20.358170.5480.1610.3880.80398.6
3.27-3.446.10.2778300.8460.1160.3020.87799.6
3.44-3.657.30.2158240.950.0810.231.18399.6
3.65-3.948.50.1648150.9770.0570.1741.4199.9
3.94-4.339.40.1298440.990.0420.1361.66999.9
4.33-4.9610.70.1068340.9960.0320.1111.84299.8
4.96-6.2410.80.1198330.9950.0350.1241.96799.6
6.24-5012.20.0698550.9980.0190.0721.7599.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZQL

5zql


Resolution: 2.9→45.234 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.87 / SU B: 22.206 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28514 393 4.8 %RANDOM
Rwork0.24735 ---
obs0.24927 7788 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.619 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å2-0 Å2
2--0.44 Å20 Å2
3----1.42 Å2
Refinement stepCycle: 1 / Resolution: 2.9→45.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 31 8 2343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192373
X-RAY DIFFRACTIONr_bond_other_d0.0020.022276
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9983200
X-RAY DIFFRACTIONr_angle_other_deg1.0135273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4935285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31223.689103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.81115447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8071521
X-RAY DIFFRACTIONr_chiral_restr0.0790.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212540
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02472
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_it5.3177.1971155
X-RAY DIFFRACTIONr_mcbond_other5.3197.1991154
X-RAY DIFFRACTIONr_mcangle_it8.7510.7651435
X-RAY DIFFRACTIONr_mcangle_other8.74810.7641436
X-RAY DIFFRACTIONr_scbond_it5.1467.8691218
X-RAY DIFFRACTIONr_scbond_other5.1447.8691219
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.66611.5351766
X-RAY DIFFRACTIONr_long_range_B_refined14.6685.5662662
X-RAY DIFFRACTIONr_long_range_B_other14.65885.5742663
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.898→2.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 29 -
Rwork0.367 524 -
obs--88.62 %

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