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- PDB-1mqf: Compound I from Proteus mirabilis catalase -

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Basic information

Entry
Database: PDB / ID: 1mqf
TitleCompound I from Proteus mirabilis catalase
ComponentsCatalase
KeywordsOXIDOREDUCTASE / alpha + beta
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 / OXYGEN ATOM / Catalase
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAndreoletti, P. / Pernoud, A. / Sainz, G. / Gouet, P. / Jouve, H.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structural studies of Proteus mirabilis catalase in its ground state, oxidized state and in complex with formic acid.
Authors: Andreoletti, P. / Pernoud, A. / Sainz, G. / Gouet, P. / Jouve, H.M.
History
DepositionSep 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
SupersessionOct 9, 2002ID: 2CAF
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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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)57,12311
Polymers55,7261
Non-polymers1,39710
Water6,990388
1
A: Catalase
hetero molecules

A: Catalase
hetero molecules

A: Catalase
hetero molecules

A: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,49344
Polymers222,9054
Non-polymers5,58840
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area50500 Å2
ΔGint-512 kcal/mol
Surface area59190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.000, 110.000, 250.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-491-

SO4

21A-491-

SO4

31A-569-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catalase /


Mass: 55726.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Proteus mirabilis (bacteria) / References: UniProt: P42321, catalase

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Non-polymers , 5 types, 398 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4-5 ℃ / pH: 7.5 / Details: Jouve, H.M., (1991) J.Mol.Biol., 221, 1075.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
127 mg/mlprotein1drop
2100 mMTris-HCl1drop
32.5 %(v/v)glycerol1drop
41 Mammonium sulfate1drop
525 mM1dropKCl
62 Mammonium sulfate1reservoir
750 mM1reservoirKCl
8100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 13, 1995
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 30822 / Num. obs: 30804 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 31.8 Å2 / Rsym value: 0.045 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 6.7 / Num. unique all: 4355 / Rsym value: 0.104 / % possible all: 98
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Num. obs: 30822 / % possible obs: 98.3 % / Num. measured all: 138931 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.104

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→14.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2559319.34 / Data cutoff high rms absF: 2559319.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1529 5 %RANDOM
Rwork0.196 ---
all0.202 30804 --
obs0.196 30775 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.5019 Å2 / ksol: 0.340027 e/Å3
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1-7.82 Å21.2 Å20 Å2
2--7.82 Å20 Å2
3----15.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 85 388 4343
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg3.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.632.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 243 5.1 %
Rwork0.246 4538 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4PARAM19.CHROMO
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.74

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