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- PDB-1si8: Crystal structure of E. faecalis catalase -

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Basic information

Entry
Database: PDB / ID: 1si8
TitleCrystal structure of E. faecalis catalase
ComponentsCatalase
KeywordsOXIDOREDUCTASE / N-terminal arm / anti-parallel beta-barrel / wrapping region / C-terminal helical region / tetramer / heme group
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / 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, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHakansson, K.O. / Brugna, M. / Tasse, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: The three-dimensional structure of catalase from Enterococcus faecalis.
Authors: Hakansson, K.O. / Brugna, M. / Tasse, L.
#1: Journal: J.Bacteriol. / Year: 2002
Title: Enterococcus faecalis heme-dependent catalase
Authors: Frankenberg, L. / Brugna, M. / Hederstedt, L.
History
DepositionFeb 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 23, 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 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)222,01618
Polymers218,7114
Non-polymers3,30514
Water21,5281195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47240 Å2
ΔGint-392 kcal/mol
Surface area57890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.86, 236.86, 198.07
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3

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Components

#1: Protein
Catalase / E.C.1.11.1.6 / catalase/peroxidase


Mass: 54677.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: katA / Plasmid: pHPSK / Production host: Bacillus subtilis (bacteria) / Strain (production host): 168A / References: UniProt: Q834P5, catalase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 1195 / 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: 4.63 Å3/Da / Density % sol: 73.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM Bis-Tris, 1.6M Lithium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.094 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 29, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.094 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 183738 / Num. obs: 183738 / % possible obs: 99.7 % / Observed criterion σ(I): -1000 / Redundancy: 3.6 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.078 / Net I/σ(I): 7.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.9 / Num. unique all: 26811 / Rsym value: 0.256 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CAE (P. mirabilis catalase)

2cae
PDB Unreleased entry


Resolution: 2.3→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 9012 -Random
Rwork0.202 ---
all0.202 183468 --
obs0.202 183468 99.8 %-
Displacement parametersBiso mean: 28.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15100 0 214 1195 16509
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0068
X-RAY DIFFRACTIONx_angle_deg1.53
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_improper_angle_d0.86

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