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- PDB-1hbz: Catalase from Micrococcus lysodeikticu -

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Basic information

Entry
Database: PDB / ID: 1hbz
TitleCatalase from Micrococcus lysodeikticu
ComponentsCATALASE
KeywordsOXIDOREDUCTASE / PEROXIDASE / IRON / HEME HYDROGEN PEROXIDE
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / 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 active site / Catalase proximal active site signature. / Catalase immune-responsive domain ...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 active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / 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 speciesMICROCOCCUS LYSODEIKTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å
AuthorsMurshudov, G.N. / Grebenko, A.I. / Barynin, V.V. / Braningen, J. / Wilson, K.S. / Dauter, Z. / Melik-Adamyan, W.R.
CitationJournal: FEBS Lett. / Year: 1992
Title: Three-Dimensional Structure of Catalase from Micrococcus Lysodeikticus at 1.5A Resolution
Authors: Murshudov, G.N. / Melik-Adamyan, W.R. / Grebenko, A.I. / Barynin, V.V. / Vagin, A.A. / Vainshtein, B.K. / Dauter, Z. / Wilson, K.S.
History
DepositionApr 24, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "A" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "A" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0193
Polymers56,3071
Non-polymers7132
Water9,692538
1
A: CATALASE
hetero molecules

A: CATALASE
hetero molecules

A: CATALASE
hetero molecules

A: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,07812
Polymers225,2284
Non-polymers2,8508
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)106.700, 106.700, 106.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2063-

HOH

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Components

#1: Protein CATALASE /


Mass: 56306.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MICROCOCCUS LYSODEIKTICUS (bacteria) / References: UniProt: P29422*PLUS, catalase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSTRUCTURE WAS SOLVED IN THE ABSENCE OF CHEMICAL SEQUENCE. PROTECT CELLS FROM THE TOXIC EFFECTS OF ...STRUCTURE WAS SOLVED IN THE ABSENCE OF CHEMICAL SEQUENCE. PROTECT CELLS FROM THE TOXIC EFFECTS OF HYDROGEN PEROXIDE BY BREAKING DOWN HYDROGEN PEROXIDE IN WATER AND OXYGEN.

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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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
pH: 5.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-30 mg/mlprotein1drop
20.6-0.8 Mammonium sulfate1drop
30.05 Msodium acetate1drop
41.2-1.4 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.98
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.501→12 Å / Num. obs: 358628 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.9
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.6 / % possible all: 96
Reflection
*PLUS
Num. obs: 95355 / Num. measured all: 358628

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Processing

Software
NameVersionClassification
REFMAC5.0.36refinement
MOSFLMdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.5→12 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.59 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12 4781 5 %RANDOM
Rwork0.092 ---
obs-90574 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Refinement stepCycle: LAST / Resolution: 1.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3981 0 48 538 4567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214220
X-RAY DIFFRACTIONr_bond_other_d0.0010.023593
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.7021.955754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.87538359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024802
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02910
X-RAY DIFFRACTIONr_nbd_refined0.2540.3736
X-RAY DIFFRACTIONr_nbd_other0.1890.33345
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.5375
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3270.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.3135
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.545
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8481.52492
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.77224027
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.59631728
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3324.51727
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.153 354
Rwork0.109 6366
Software
*PLUS
Name: REFMAC_5.0.36 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.12 / Rfactor Rwork: 0.092
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONp_bond_d0.0130.021
X-RAY DIFFRACTIONp_angle_d0.0010.02

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