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Basic information

Entry
Database: PDB / ID: 5gkn
TitleCatalase structure determined by electron crystallography of thin 3D crystals
ComponentsCatalase
KeywordsOXIDOREDUCTASE / HEME / NADPH
Function / homology
Function and homology information


Detoxification of Reactive Oxygen Species / catalase complex / cellular detoxification of hydrogen peroxide / Peroxisomal protein import / catalase / catalase activity / Neutrophil degranulation / positive regulation of cell division / hydrogen peroxide catabolic process / response to hydrogen peroxide ...Detoxification of Reactive Oxygen Species / catalase complex / cellular detoxification of hydrogen peroxide / Peroxisomal protein import / catalase / catalase activity / Neutrophil degranulation / positive regulation of cell division / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / heme binding / enzyme binding / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Cytochrome C Oxidase; Chain J / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. ...Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Cytochrome C Oxidase; Chain J / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Few Secondary Structures / Irregular / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / Catalase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3.2 Å
AuthorsYonekura, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2015
Title: Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.
Authors: Koji Yonekura / Kazuyuki Kato / Mitsuo Ogasawara / Masahiro Tomita / Chikashi Toyoshima /
Abstract: Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for ...Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2015
Title: Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.
Authors: Koji Yonekura / Kazuyuki Kato / Mitsuo Ogasawara / Masahiro Tomita / Chikashi Toyoshima /
Abstract: Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for ...Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.
History
DepositionJul 4, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 26, 2016ID: 3J7U
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / em_image_scans / em_software / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_software.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Catalase
B: Catalase
C: Catalase
D: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,44412
Polymers239,9974
Non-polymers5,4488
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51110 Å2
ΔGint-292 kcal/mol
Surface area63910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.000, 173.500, 206.000
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
Catalase /


Mass: 59999.160 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00432, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 58
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: catalase / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Bos taurus (cattle)
Buffer solutionpH: 5.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE
Crystal growpH: 5.3

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Data collection

MicroscopyModel: HITACHI EF3000
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 0.01 e/Å2 / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k)
EM diffractionCamera length: 3450 mm
EM diffraction shellResolution: 3.2→20 Å / Fourier space coverage: 73 % / Multiplicity: 46.3 / Num. of structure factors: 30337 / Phase residual: 23.7 °
EM diffraction statsFourier space coverage: 73 % / High resolution: 3.2 Å / Num. of intensities measured: 10000 / Num. of structure factors: 30337 / Phase error: 23.7 ° / Phase residual: 23.7 ° / Phase error rejection criteria: unknown / Rmerge: 33.2 / Rsym: 10

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
EDINTLATOPT SCALEPACKdata scaling
Modified version of phenixphasing
Modifiedversion ofphasing
EM softwareName: PHENIX / Category: model fitting
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 69 Å / B: 173.5 Å / C: 206 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionSymmetry type: 3D CRYSTAL
RefinementStarting model: 3NWL

3nwl


Resolution: 3.2→19.988 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.81 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3043 844 2.78 %
Rwork0.2505 --
obs0.252 30337 73.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00716956
ELECTRON CRYSTALLOGRAPHYf_angle_d0.88523124
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d13.40610020
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0482336
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0063060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.39960.32171390.2344841ELECTRON CRYSTALLOGRAPHY73
3.3996-3.66060.32041380.24014835ELECTRON CRYSTALLOGRAPHY73
3.6606-4.02630.32271390.24554858ELECTRON CRYSTALLOGRAPHY73
4.0263-4.60270.28491400.26194900ELECTRON CRYSTALLOGRAPHY73
4.6027-5.77560.29791430.25614955ELECTRON CRYSTALLOGRAPHY73
5.7756-19.98790.28061450.26215104ELECTRON CRYSTALLOGRAPHY73

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