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- PDB-3uw8: Crystal Structure Analysis of the Ser305Thr Variants of KatG from... -

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Basic information

Entry
Database: PDB / ID: 3uw8
TitleCrystal Structure Analysis of the Ser305Thr Variants of KatG from Haloarcula marismortui
ComponentsCatalase-peroxidase 2
KeywordsOXIDOREDUCTASE / CATALASE-PEROXIDASE
Function / homology
Function and homology information


catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / cellular response to hydrogen peroxide / heme binding / metal ion binding / cytosol
Similarity search - Function
Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase ...Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase-peroxidase 2
Similarity search - Component
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSato, T. / Higuchi, W. / Yoshimatsu, K. / Fujiwara, T.
CitationJournal: To be Published
Title: Catalatic Implication Guided by Structure, Kinetics and Theoretical Studies on Ser305Thr and Arg409Leu Variants of HmKatG
Authors: Sato, T. / Higuchi, W. / Yoshimatsu, K. / Fujiwara, T.
History
DepositionDec 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catalase-peroxidase 2
B: Catalase-peroxidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,8394
Polymers164,6062
Non-polymers1,2332
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-75 kcal/mol
Surface area51530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)315.410, 81.120, 75.020
Angle α, β, γ (deg.)90.00, 99.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Catalase-peroxidase 2 / KatG / CP 2 / Peroxidase/catalase 2


Mass: 82303.211 Da / Num. of mol.: 2 / Mutation: S305T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / Gene: katG2 / Production host: Haloferax volcanii (archaea) / References: UniProt: O59651, catalase-peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.36-2.58M Ammonium sulfate, 0.5M potassium chloride, 20mM sodium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 14, 2005
RadiationMonochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. all: 77588 / Num. obs: 77588 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 9.1
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
CrystalCleardata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→24.81 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2939564.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.309 3920 5.1 %RANDOM
Rwork0.257 ---
obs0.257 77588 99.5 %-
all-77588 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.5993 Å2 / ksol: 0.332901 e/Å3
Displacement parametersBiso mean: 45.9 Å2
Baniso -1Baniso -2Baniso -3
1--14.67 Å20 Å2-7.98 Å2
2--0.13 Å20 Å2
3---14.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.35→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11242 0 86 235 11563
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.35→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.388 451 5.2 %
Rwork0.374 8142 -
obs--62.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4hem_xplor.paramhem_xplor.top
X-RAY DIFFRACTION5sha_xplor_param.txtsha_xplor_top.txt

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