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- PDB-3vlj: Crystal Structure Analysis of the Cyanide Arg409Leu Variant Compl... -

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Basic information

Entry
Database: PDB / ID: 3vlj
TitleCrystal Structure Analysis of the Cyanide Arg409Leu Variant Complexes with o-Dianisidine in 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
CYANIDE ION / 3,3'-dimethoxybiphenyl-4,4'-diamine / PROTOPORPHYRIN IX CONTAINING FE / Catalase-peroxidase 2
Similarity search - Component
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSato, T. / Higuchi, W. / Yoshimatsu, K. / Fujiwara, T.
CitationJournal: To be Published
Title: Crystal Structures and Peroxidatic Function of Cyanide Arg409Leu Variant and its Complexes with o-Dianisidine in KatG from HALOARCULA MARISMORTUI
Authors: Sato, T. / Higuchi, W. / Yoshimatsu, K. / Fujiwara, T.
History
DepositionDec 1, 2011Deposition site: PDBJ / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)166,2648
Polymers164,4902
Non-polymers1,7746
Water13,457747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-75 kcal/mol
Surface area51000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)315.209, 80.762, 75.433
Angle α, β, γ (deg.)90.00, 99.50, 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: 82245.148 Da / Num. of mol.: 2 / Mutation: R409L
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: Chemical ChemComp-DDJ / 3,3'-dimethoxybiphenyl-4,4'-diamine / o-Dianisidine


Mass: 244.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N2O2
#4: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1mM o-Dianisidine, 2.36-2.58M Ammonium sulfate, 0.5M potassium chloride, 20mM sodium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 16, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 203754 / Num. obs: 203754 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 39.2
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.74 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 0.57 / Data cutoff high absF: 2928338 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: FOR DDJ (ODA) SUBSTRATE, CYANIDE ARG409LEU VARIANT HAS HIGHER BINDING ENERGY IN THE CHAIN A THAN THAT OF THE CHAIN B DUE TO THE INTRINSIC FLEXIBILITY OF ODA WITH THE LARGER B-FACTOR AND LOWER OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 10041 4.9 %RANDOM
Rwork0.216 ---
obs-203754 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1006 Å2 / ksol: 0.3976 e/Å3
Displacement parametersBiso max: 65.6 Å2 / Biso mean: 24.8222 Å2 / Biso min: 2.62 Å2
Baniso -1Baniso -2Baniso -3
1--5.39 Å20 Å2-3.03 Å2
2--0.07 Å20 Å2
3---5.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11121 0 126 747 11994
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 1612 4.9 %
Rwork0.254 31181 -
all-32793 -
obs--96.4 %
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 DIFFRACTION5cn.parcn.top

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