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- PDB-3vll: Crystal Structure Analysis of the Ser305Ala variant of KatG from ... -

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Basic information

Entry
Database: PDB / ID: 3vll
TitleCrystal Structure Analysis of the Ser305Ala variant of KatG from HALOARCULA MARISMORTUI Complexes with Inhibitor SHA
ComponentsCatalase-peroxidase 2
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / CATALASE-PEROXIDASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding
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 / SALICYLHYDROXAMIC ACID / Catalase-peroxidase 2
Similarity search - Component
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSato, T. / Higuchi, W. / Yoshimatsu, K. / Fujiwara, T.
CitationJournal: To be Published
Title: Crystal Structure and Kinetics Studies on Ser305Ala variant of KatG from HALOARCULA MARISMORTUI and its Complexes with Inhibitor SHA
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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)166,0866
Polymers164,5462
Non-polymers1,5394
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-61 kcal/mol
Surface area50050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.187, 76.320, 140.235
Angle α, β, γ (deg.)90.00, 92.32, 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: 82273.188 Da / Num. of mol.: 2 / Mutation: S305A
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 / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SHA / SALICYLHYDROXAMIC ACID / Salicylhydroxamic acid


Mass: 153.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO3 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1mM SHA, 2.92-3.0M ammonium sulfate, 0.5M potassium chloride, 20mM sodium phosphate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 17, 2007
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: 1.98→50 Å / Num. all: 105746 / Num. obs: 105746 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 13.6
Reflection shellResolution: 1.98→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 0.61 / % possible all: 98.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.36 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.74 / Data cutoff high absF: 2910630 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: FOR STRONG INHIBITORS (SHA), THE HIGHER B-FACTOR AND LOWER OCCUPANCY IN SER305ALA VARIANT CORRELATED WITH THE HIGHER BINDING ENERGIES OF CHAIN B AS COMPARED WITH CHAIN A, ESPECIALLY AT LOW ...Details: FOR STRONG INHIBITORS (SHA), THE HIGHER B-FACTOR AND LOWER OCCUPANCY IN SER305ALA VARIANT CORRELATED WITH THE HIGHER BINDING ENERGIES OF CHAIN B AS COMPARED WITH CHAIN A, ESPECIALLY AT LOW SHA LIGAND CONCENTRATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 5258 5 %RANDOM
Rwork0.247 ---
obs-105746 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.6646 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso max: 80.54 Å2 / Biso mean: 35.9258 Å2 / Biso min: 14.19 Å2
Baniso -1Baniso -2Baniso -3
1-7.63 Å20 Å25.59 Å2
2---4.22 Å20 Å2
3----3.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11133 0 108 242 11483
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 856 5 %
Rwork0.273 16384 -
all-17240 -
obs--97.1 %
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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