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- PDB-4oua: Coexistent single-crystal structure of latent and active mushroom... -

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Basic information

Entry
Database: PDB / ID: 4oua
TitleCoexistent single-crystal structure of latent and active mushroom tyrosinase (abPPO4) mediated by a hexatungstotellurate(VI)
Components
  • latent form of PPO4 Tyrosinase
  • proteolytically activated form of PPO4 Tyrosinase
KeywordsOXIDOREDUCTASE / type-3 copper protein / tyrosinase / PPO4 / zymogen / tyrosinase maturation / hetero-protein co-crystallization / Anderson-Evans-type polyoxometalate
Function / homologydi-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Orthogonal Bundle / Mainly Alpha / COPPER (I) ION / 6-tungstotellurate(VI) / :
Function and homology information
Biological speciesAgaricus bisporus var. bisporus H97 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.763 Å
AuthorsSt.Mauracher, G. / Molitor, C. / Al-Oweini, R. / Kortz, U. / Rompel, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Latent and active abPPO4 mushroom tyrosinase cocrystallized with hexatungstotellurate(VI) in a single crystal.
Authors: Mauracher, S.G. / Molitor, C. / Al-Oweini, R. / Kortz, U. / Rompel, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystallization and preliminary X-ray crystallographic analysis of latent isoform PPO4 mushroom (Agaricus bisporus) tyrosinase.
Authors: Mauracher, S.G. / Molitor, C. / Al-Oweini, R. / Kortz, U. / Rompel, A.
#2: Journal: Phytochemistry / Year: 2014
Title: High level protein-purification allows the unambiguous polypeptide determination of latent isoform PPO4 of mushroom tyrosinase.
Authors: Mauracher, S.G. / Molitor, C. / Michael, C. / Kragl, M. / Rizzi, A. / Rompel, A.
History
DepositionFeb 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jan 31, 2018Group: Source and taxonomy / Category: entity_src_nat / Item: _entity_src_nat.pdbx_organism_scientific

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: proteolytically activated form of PPO4 Tyrosinase
B: latent form of PPO4 Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,43516
Polymers107,3712
Non-polymers4,06414
Water2,324129
1
A: proteolytically activated form of PPO4 Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6196
Polymers43,7321
Non-polymers1,8875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: latent form of PPO4 Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,81610
Polymers63,6391
Non-polymers2,1779
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)213.530, 83.720, 66.950
Angle α, β, γ (deg.)90.000, 102.530, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-609-

TEW

21B-609-

TEW

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein proteolytically activated form of PPO4 Tyrosinase


Mass: 43731.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: White edible mushroom
Source: (natural) Agaricus bisporus var. bisporus H97 (fungus)
Strain: strain H97 / ATCC MYA-4626 / FGSC 10389 / References: UniProt: K9I869, tyrosinase
#2: Protein latent form of PPO4 Tyrosinase


Mass: 63639.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: White edible mushroom
Source: (natural) Agaricus bisporus var. bisporus H97 (fungus)
Strain: strain H97 / ATCC MYA-4626 / FGSC 10389 / References: UniProt: K9I869, tyrosinase

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Non-polymers , 5 types, 143 molecules

#3: Chemical
ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O24TeW6
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG4000, 1 mM Na6[TeW6O24].22H2O, 25 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 15, 2013
RadiationMonochromator: single bounce monochromator (22m) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.76→48.132 Å / Num. all: 28294 / % possible obs: 92.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 44.95 Å2 / Rmerge(I) obs: 0.129 / Χ2: 1.206 / Net I/σ(I): 6.53
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.76-2.840.6071.4970853502182.4
2.84-2.910.5411.6985804048195.4
2.91-30.4581.9580803867195.3
3-3.090.4022.2780033830196.2
3.09-3.190.3462.777303669195.5
3.19-3.30.273.1972223467195.1
3.3-3.430.2064.2370873353194
3.43-3.570.1784.9766383185192
3.57-3.730.1336.1760752962189.7
3.73-3.910.117.2250652537180.6
3.91-4.120.0978.1961322942196.5
4.12-4.370.089.9357512695196.7
4.37-4.670.07210.8354792590196.4
4.67-5.050.06411.9350412361195.1
5.05-5.530.07211.0745482150194.1
5.53-6.180.07510.2939181853190.7
6.18-7.130.06411.433511625188.2
7.13-8.740.04216.227481324186.3
8.74-12.360.02724.0824751164198.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
GDA(Generic Data Acquisition)data collection
XDSdata reduction
PHENIXPhaser (MR)phasing
RefinementResolution: 2.763→48.132 Å / FOM work R set: 0.8407 / SU ML: 0.37 / σ(F): 1.35 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 1415 5 %
Rwork0.186 26875 -
obs0.1881 28290 95.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.13 Å2 / Biso mean: 42.93 Å2 / Biso min: 18.88 Å2
Refinement stepCycle: LAST / Resolution: 2.763→48.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7521 0 102 129 7752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117898
X-RAY DIFFRACTIONf_angle_d0.58710861
X-RAY DIFFRACTIONf_chiral_restr0.0261127
X-RAY DIFFRACTIONf_plane_restr0.0031381
X-RAY DIFFRACTIONf_dihedral_angle_d10.8922796
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7632-2.86190.34971310.28052491262289
2.8619-2.97650.32321440.26172744288898
2.9765-3.11190.29421450.24642741288698
3.1119-3.27590.2911440.21972747289198
3.2759-3.48110.26071420.20042691283396
3.4811-3.74980.23591390.18592644278394
3.7498-4.1270.20171350.16122565270091
4.127-4.72370.17771450.14242751289698
4.7237-5.94970.1781460.16172783292998
5.9497-48.13960.19741440.17162718286294

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