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- PDB-3j7b: Catalase solved at 3.2 Angstrom resolution by MicroED -

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Basic information

Entry
Database: PDB / ID: 3j7b
TitleCatalase solved at 3.2 Angstrom resolution by MicroED
ComponentsCatalase
KeywordsOXIDOREDUCTASE
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
AuthorsNannenga, B.L. / Shi, D. / Hattne, J. / Reyes, F.E. / Gonen, T.
CitationJournal: Elife / Year: 2014
Title: Structure of catalase determined by MicroED.
Authors: Brent L Nannenga / Dan Shi / Johan Hattne / Francis E Reyes / Tamir Gonen /
Abstract: MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of ...MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination.
History
DepositionJun 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Other
Revision 1.2Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / em_image_scans / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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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
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54220 Å2
ΔGint-309 kcal/mol
Surface area59110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.842, 172.081, 182.067
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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Bovine liver catalase / Type: COMPLEX
Buffer solutionpH: 6.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jun 15, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 0.1 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→125.061 Å / Num. all: 36043 / Num. obs: 28101

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Processing

SoftwareName: REFMAC / Version: 5.8.0075 / Classification: refinement
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.2 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
RefinementResolution: 3.2→125.06 Å / Cor.coef. Fo:Fc: 0.795 / Cor.coef. Fo:Fc free: 0.745 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.853 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3079 1369 4.9 %RANDOM
Rwork0.2621 26732 --
obs0.2644 28101 77.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 34.26 Å2 / Biso mean: 22.123 Å2 / Biso min: 16.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0 Å2-0 Å2
2---2.26 Å20 Å2
3---3.44 Å2
Refinement stepCycle: LAST / Resolution: 3.2→125.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16068 0 364 0 16432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.010.01916956
ELECTRON CRYSTALLOGRAPHYr_bond_other_d00.0215384
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.2321.96823124
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg3.501335360
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg5.19751992
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg33.65123.665884
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg14.73152596
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_4_deg19.80215124
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0570.22336
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.010.02119520
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other0.0270.024292
ELECTRON CRYSTALLOGRAPHYr_mcbond_it0.3292.2347980
ELECTRON CRYSTALLOGRAPHYr_mcbond_other0.3292.2347979
ELECTRON CRYSTALLOGRAPHYr_mcangle_it0.513.3519968
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 90 -
Rwork0.348 1688 -
all-1778 -
obs--68.6 %

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