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- PDB-1p7z: Crystal structure of the D181S variant of catalase HPII from E. coli -

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Basic information

Entry
Database: PDB / ID: 1p7z
TitleCrystal structure of the D181S variant of catalase HPII from E. coli
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / catalase / beta barrel / channel
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
Catalase, four-helical domain / 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 / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. ...Catalase, four-helical domain / 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 / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core 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 (GATase) domain / Class I glutamine amidotransferase-like / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsChelikani, P. / Carpena, X. / Fita, I. / Loewen, P.C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: An electrical potential in the access channel of catalases enhances catalysis
Authors: Chelikani, P. / Carpena, X. / Fita, I. / Loewen, P.C.
History
DepositionMay 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)339,4408
Polymers336,9744
Non-polymers2,4664
Water49,2352733
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58470 Å2
ΔGint-274 kcal/mol
Surface area78640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.34, 132.88, 121.45
Angle α, β, γ (deg.)90.00, 109.4, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Catalase HPII / Hydroxyperoxidase II


Mass: 84243.438 Da / Num. of mol.: 4 / Mutation: D181S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: katE / Plasmid: pD181S / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / References: UniProt: P21179, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 2733 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 3350, LiCl, Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115-17 %PEG33501reservoir
21.6-1.7 M1reservoirLiCl
30.1 MTris1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9762 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 21, 2001
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→29.8 Å / Num. all: 138852 / Num. obs: 138852 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.8 / Num. unique all: 13805 / Rsym value: 0.33 / % possible all: 99.5
Reflection
*PLUS
Num. obs: 138759 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 99.5 % / Num. unique obs: 11109

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GGE

1gge


Resolution: 2.21→29.8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 6965 -Random
Rwork0.144 ---
all0.154 138642 --
obs0.148 138642 99.6 %-
Displacement parametersBiso mean: 22.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2.21→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22988 0 172 2733 25893
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.012
X-RAY DIFFRACTIONr_angle_refined_deg2
X-RAY DIFFRACTIONr_gen_planes_refined0.023
LS refinement shellResolution: 2.2→2.27 Å
RfactorNum. reflection% reflection
Rfree0.252 590 -
Rwork0.174 --
obs-11109 99.5 %
Refinement
*PLUS
Highest resolution: 2.2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.012
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg2

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