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- PDB-8j4q: Crystal structure of eKatE (extra KatE) from atypical E. coli -

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Basic information

Entry
Database: PDB / ID: 8j4q
TitleCrystal structure of eKatE (extra KatE) from atypical E. coli
Components(Catalase) x 2
KeywordsOXIDOREDUCTASE / eKatE / KatE / catalase / oxido-reductase / HEME
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytosol
Similarity search - Function
Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Catalase, mono-functional, haem-containing, clade 2, helical domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain ...Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Catalase, mono-functional, haem-containing, clade 2, helical 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 / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYoo, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of eKatE (extra KatE) from atypical E. coli
Authors: Yoo, Y.
History
DepositionApr 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)340,3918
Polymers337,9254
Non-polymers2,4664
Water24,7351373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59840 Å2
ΔGint-273 kcal/mol
Surface area79460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.585, 178.935, 107.279
Angle α, β, γ (deg.)90.000, 106.700, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Catalase


Mass: 84493.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: B2H83_27520 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I8WFM0, catalase
#2: Protein Catalase


Mass: 84477.250 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: B2H83_27520 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I8WFM0, catalase
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1373 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium cacodylate, 40% MPD, PEG8000 5%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→47.49 Å / Num. obs: 156082 / % possible obs: 97.13 % / Redundancy: 1.9 % / Biso Wilson estimate: 31.76 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.06432 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.4847 / Mean I/σ(I) obs: 1.72 / Num. unique obs: 15567 / CC1/2: 0.643

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.49 Å / SU ML: 0.2735 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.9509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2134 1262 0.97 %
Rwork0.1728 154758 -
obs0.1731 156020 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23018 0 172 1373 24563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009923982
X-RAY DIFFRACTIONf_angle_d1.012132598
X-RAY DIFFRACTIONf_chiral_restr0.0593404
X-RAY DIFFRACTIONf_plane_restr0.00914306
X-RAY DIFFRACTIONf_dihedral_angle_d16.55478874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.37581370.285417144X-RAY DIFFRACTION96.98
2.18-2.280.31151420.268817136X-RAY DIFFRACTION97.15
2.28-2.40.30561400.233417240X-RAY DIFFRACTION97.48
2.4-2.550.29661430.208917287X-RAY DIFFRACTION97.7
2.55-2.750.23421400.193617273X-RAY DIFFRACTION97.81
2.75-3.030.23291370.178817261X-RAY DIFFRACTION97.68
3.03-3.470.19281390.158117120X-RAY DIFFRACTION96.59
3.47-4.370.1581360.132916834X-RAY DIFFRACTION95.1
4.37-47.490.17191480.144417463X-RAY DIFFRACTION97.74

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