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- PDB-6ztx: Crystal Structure of catalase HPII from Escherichia coli (serendi... -

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Basic information

Entry
Database: PDB / ID: 6ztx
TitleCrystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / catalase / hydrogen-peroxide / heme / iron / oxidative stress / artifact crystallization / impurities / contaminations
Function / homology
Function and homology information


catalase / catalase activity / hyperosmotic response / hydrogen peroxide catabolic process / response to oxidative stress / iron ion binding / heme binding / DNA damage response / identical protein binding / cytosol / cytoplasm
Similarity search - Function
C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site ...C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGrzechowiak, M. / Sekula, B. / Ruszkowski, M.
Funding support Poland, United States, 3items
OrganizationGrant numberCountry
Polish National Science CentreSONATA 2018/31/D/NZ1/03630 Poland
Polish National Science CentreSYMFONIA 2016/20/W/ST5/00478 Poland
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: Acta Biochim.Pol. / Year: 2021
Title: Serendipitous crystallization of E. coli HPII catalase, a sequel to "the tale usually not told".
Authors: Grzechowiak, M. / Sekula, B. / Jaskolski, M. / Ruszkowski, M.
History
DepositionJul 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Mar 3, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.4Mar 31, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Jan 31, 2024Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)339,90919
Polymers336,5774
Non-polymers3,33315
Water59,6123309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61730 Å2
ΔGint-265 kcal/mol
Surface area78950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.213, 132.926, 121.650
Angle α, β, γ (deg.)90.000, 109.651, 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 HPII / Hydroxyperoxidase II


Mass: 84144.148 Da / Num. of mol.: 4 / Mutation: R37S, S99D, K372N, R521S / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: P21179, catalase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-HDD / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME


Mass: 632.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 670790 / % possible obs: 98.3 % / Redundancy: 4.84 % / Biso Wilson estimate: 11.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.115 / Net I/σ(I): 11.78
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 4.86 % / Rmerge(I) obs: 1.101 / Mean I/σ(I) obs: 2 / Num. unique obs: 106698 / CC1/2: 0.59 / Rrim(I) all: 1.236 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gge

1gge


Resolution: 1.3→44.76 Å / SU ML: 0.1299 / Cross valid method: FREE R-VALUE / σ(F): 0.69 / Phase error: 15.797
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1623 2638 -
Rwork0.1345 1318755 -
obs0.1345 668130 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.76 Å2
Refinement stepCycle: LAST / Resolution: 1.3→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22948 0 228 3309 26485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005124285
X-RAY DIFFRACTIONf_angle_d1.080733164
X-RAY DIFFRACTIONf_chiral_restr0.07923484
X-RAY DIFFRACTIONf_plane_restr0.00584457
X-RAY DIFFRACTIONf_dihedral_angle_d15.62189101

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