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- PDB-8bbr: Determination of the structure of active tyrosinase from bacteriu... -

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Basic information

Entry
Database: PDB / ID: 8bbr
TitleDetermination of the structure of active tyrosinase from bacterium Verrucomicrobium spinosum
ComponentsCore tyrosinase
KeywordsMETAL BINDING PROTEIN / Tyrosinase / Copper / Verrucomicrobium spinosum / PPO
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciesVerrucomicrobium spinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsFekry, M. / Dave, K. / Badgujar, D. / Aurelius, O. / Hamnevik, E. / Dobritzsch, D. / Danielson, H.
Funding support China, 1items
OrganizationGrant numberCountry
Other private China
CitationJournal: Biomolecules / Year: 2023
Title: The Crystal Structure of Tyrosinase from Verrucomicrobium spinosum Reveals It to Be an Atypical Bacterial Tyrosinase.
Authors: Fekry, M. / Dave, K.K. / Badgujar, D. / Hamnevik, E. / Aurelius, O. / Dobritzsch, D. / Danielson, U.H.
History
DepositionOct 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Core tyrosinase
B: Core tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,50316
Polymers73,5162
Non-polymers98714
Water12,394688
1
A: Core tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2688
Polymers36,7581
Non-polymers5107
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Core tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2358
Polymers36,7581
Non-polymers4777
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.298, 63.443, 117.311
Angle α, β, γ (deg.)90.000, 97.250, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1A
d_2ens_1B

NCS domain segments:

Ens-ID: ens_1 / End auth comp-ID: PRO / End label comp-ID: PRO

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLNGLNAA34 - 3511 - 318
d_22ALAALABB36 - 3513 - 318

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Components

#1: Protein Core tyrosinase


Mass: 36757.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verrucomicrobium spinosum (bacteria) / Production host: Escherichia coli (E. coli) / References: tyrosinase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M ammonium sulfate, 0.1 M MES pH 6.5, 30% w/v PEG5000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.64→116.37 Å / Num. obs: 75699 / % possible obs: 98.2 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 9.8
Reflection shellResolution: 1.64→1.67 Å / Num. unique obs: 3073 / CC1/2: 0.362

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX5.8.0238refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z11, 4Z12, 5CE9

4z11

4z12

5ce9


Resolution: 1.64→116.37 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.723 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 3875 5.2 %RANDOM
Rwork0.1904 ---
obs0.1922 71195 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.95 Å2 / Biso mean: 25.752 Å2 / Biso min: 10.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å2-0 Å20.74 Å2
2---1.32 Å20 Å2
3----2.01 Å2
Refinement stepCycle: final / Resolution: 1.64→116.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5179 0 26 692 5897
Biso mean--46.21 36.08 -
Num. residues----643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125429
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174643
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.6477408
X-RAY DIFFRACTIONr_angle_other_deg1.4061.56910768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.895651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39821.646328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64915765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6531541
X-RAY DIFFRACTIONr_chiral_restr0.0960.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021310
Refine LS restraints NCS

Ens-ID: ens_1 / Number: 11706 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.64→1.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5 217 -
Rwork0.455 3846 -
all-4063 -
obs--71.41 %

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