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- PDB-2cwl: Crystal structure of manganese-free form of pseudocatalase from T... -

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Basic information

Entry
Database: PDB / ID: 2cwl
TitleCrystal structure of manganese-free form of pseudocatalase from Thermus thermophilus HB8
Componentsmanganese-free pseudocatalase
KeywordsOXIDOREDUCTASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Manganese catalase / Manganese catalase, ferritin-like di-iron-binding domain / Manganese containing catalase / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Manganese-containing pseudocatalase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsEbihara, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structural and functional analysis of pseudocatalase from Thermus thermophilus HB8
Authors: Ebihara, A. / Yokoyama, S. / Kuramitsu, S.
History
DepositionJun 21, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: manganese-free pseudocatalase
B: manganese-free pseudocatalase


Theoretical massNumber of molelcules
Total (without water)66,7462
Polymers66,7462
Non-polymers00
Water7,963442
1
A: manganese-free pseudocatalase
B: manganese-free pseudocatalase

A: manganese-free pseudocatalase
B: manganese-free pseudocatalase

A: manganese-free pseudocatalase
B: manganese-free pseudocatalase


Theoretical massNumber of molelcules
Total (without water)200,2396
Polymers200,2396
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area42100 Å2
ΔGint-267 kcal/mol
Surface area45630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.360, 131.360, 131.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein manganese-free pseudocatalase


Mass: 33373.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SM21, catalase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.8 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 40% PEG400, 0.1M Tris-HCl, 0.25M Li sulfate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 29, 2004
RadiationMonochromator: SI DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→46.44 Å / Num. obs: 90305 / % possible obs: 99.8 % / Redundancy: 19.14 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 21.1
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 9.36 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 6 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→43.79 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3229123.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.181 9037 10 %RANDOM
Rwork0.166 ---
all0.167 ---
obs0.166 90304 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.3765 Å2 / ksol: 0.400672 e/Å3
Displacement parametersBiso mean: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.65→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4641 0 0 442 5083
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.791.5
X-RAY DIFFRACTIONc_mcangle_it1.132
X-RAY DIFFRACTIONc_scbond_it1.552
X-RAY DIFFRACTIONc_scangle_it2.242.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.229 1506 10.1 %
Rwork0.202 13399 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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