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- PDB-1u2j: Crystal structure of the C-terminal domain from the catalase-pero... -

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Basic information

Entry
Database: PDB / ID: 1u2j
TitleCrystal structure of the C-terminal domain from the catalase-peroxidase KatG of Escherichia coli (P21 21 21)
ComponentsPeroxidase/catalase HPI
KeywordsOXIDOREDUCTASE / KatG / catalase-peroxidase / C-terminal domain
Function / homology
Function and homology information


catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / peroxidase activity / cellular response to hydrogen peroxide / response to oxidative stress / oxidoreductase activity / heme binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase ...Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCarpena, X. / Melik-Adamyan, W. / Loewen, P.C. / Fita, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the C-terminal domain of the catalase-peroxidase KatG from Escherichia coli.
Authors: Carpena, X. / Melik-Adamyan, W. / Loewen, P.C. / Fita, I.
History
DepositionJul 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxidase/catalase HPI
B: Peroxidase/catalase HPI
C: Peroxidase/catalase HPI
D: Peroxidase/catalase HPI
E: Peroxidase/catalase HPI
F: Peroxidase/catalase HPI
G: Peroxidase/catalase HPI
H: Peroxidase/catalase HPI


Theoretical massNumber of molelcules
Total (without water)285,1948
Polymers285,1948
Non-polymers00
Water00
1
A: Peroxidase/catalase HPI


Theoretical massNumber of molelcules
Total (without water)35,6491
Polymers35,6491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxidase/catalase HPI


Theoretical massNumber of molelcules
Total (without water)35,6491
Polymers35,6491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peroxidase/catalase HPI


Theoretical massNumber of molelcules
Total (without water)35,6491
Polymers35,6491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peroxidase/catalase HPI


Theoretical massNumber of molelcules
Total (without water)35,6491
Polymers35,6491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Peroxidase/catalase HPI


Theoretical massNumber of molelcules
Total (without water)35,6491
Polymers35,6491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Peroxidase/catalase HPI


Theoretical massNumber of molelcules
Total (without water)35,6491
Polymers35,6491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Peroxidase/catalase HPI


Theoretical massNumber of molelcules
Total (without water)35,6491
Polymers35,6491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Peroxidase/catalase HPI


Theoretical massNumber of molelcules
Total (without water)35,6491
Polymers35,6491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.208, 98.699, 302.821
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
Peroxidase/catalase HPI / Catalase-peroxidase / Hydroperoxidase I


Mass: 35649.207 Da / Num. of mol.: 8 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: katG / Production host: Escherichia coli (E. coli) / References: UniProt: P13029, catalase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.6 M Sodium Citrate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97395 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2001 / Details: Mirrors
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97395 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 135504 / Num. obs: 135504 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.087
Reflection shellResolution: 2.1→2.2 Å / Num. unique all: 17775 / Rsym value: 0.18 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1u2k

1u2k


Resolution: 2.3→19.96 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.873 / SU B: 8.961 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.564 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32668 10340 10 %RANDOM
Rwork0.2332 ---
all0.24264 92771 --
obs0.24264 92771 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.123 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2---1.03 Å20 Å2
3---1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18136 0 0 0 18136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02118456
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.95425016
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7552352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.22848
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214024
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3030.29899
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2925
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4420.2217
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5250.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.044211696
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.517418712
X-RAY DIFFRACTIONr_scbond_it4.80846760
X-RAY DIFFRACTIONr_scangle_it6.60166304
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.386 777
Rwork0.248 6911

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