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- PDB-5np1: Open protomer of human ATM (Ataxia telangiectasia mutated) -

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Basic information

Entry
Database: PDB / ID: 5np1
TitleOpen protomer of human ATM (Ataxia telangiectasia mutated)
DescriptorSerine-protein kinase ATM (E.C.2.7.11.1)
KeywordsTRANSFERASE / FAT / MRN / DNA-repair / HEAT-repeats / Transferase
Specimen sourceHomo sapiens / human
MethodElectron microscopy (5.7 A resolution / Single particle)
AuthorsBaretic, D. / Pollard, H.K. / Fisher, D.I. / Johnson, C.M. / Santhanam, B. / Truman, C.M. / Kouba, T. / Fersht, A.R. / Phillips, C. / Williams, R.L.
CitationSci Adv, 2017, 3, e1700933-e1700933

Sci Adv, 2017, 3, e1700933-e1700933 StrPapers
Structures of closed and open conformations of dimeric human ATM.
Domagoj Baretić / Hannah K Pollard / David I Fisher / Christopher M Johnson / Balaji Santhanam / Caroline M Truman / Tomas Kouba / Alan R Fersht / Christopher Phillips / Roger L Williams

DateDeposition: Apr 13, 2017 / Release: May 17, 2017

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Assembly

Deposited unit
A: Serine-protein kinase ATM


Theoretical massNumber of molelcules
Total (without water)352,3941
Polyers352,3941
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)Serine-protein kinase ATM / Ataxia telangiectasia mutated / A-T mutated


Mass: 352393.969 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: Q13315, EC: 2.7.11.1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
Type: ORGANELLE OR CELLULAR COMPONENT
Specimen supportGrid material: GOLD / Grid mesh size: 300 /inch. / Grid type: Quantifoil or UltrAuFoil R 1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100
Details: 3 uL sample/grid blotted for 12 s before plunge-freezing

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 97902 X / Calibrated magnification: 35714 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 80.15 K

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
ComputingStructure refinement: PHENIX (1.10.1_2155: phenix.real_space_refine)
3D reconstructionResolution: 5.7 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 60556 / Number of class averages: 2
Atomic model buildingRef space: REAL
Refine LS restraints
Refine idTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01312184
ELECTRON MICROSCOPYf_angle_d1.38916923
ELECTRON MICROSCOPYf_dihedral_angle_d7.8577153
ELECTRON MICROSCOPYf_chiral_restr0.0532367
ELECTRON MICROSCOPYf_plane_restr0.0092419

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