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- PDB-6rrr: Crystal structure of the tyrosinase PvdP from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6rrr
TitleCrystal structure of the tyrosinase PvdP from Pseudomonas aeruginosa
ComponentsPvdP
KeywordsOXIDOREDUCTASE / tyrosinase / pyoverdine
Function / homologypyoverdine biosynthetic process / tyrosinase activity / Di-copper centre-containing domain superfamily / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / metal ion binding / PvdP
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.11 Å
AuthorsWibowo, J.P. / Batista, F.A. / van Oosterwijk, N. / Groves, M.R. / Dekker, F.J. / Quax, W.J.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: A novel mechanism of inhibition by phenylthiourea on PvdP, a tyrosinase synthesizing pyoverdine of Pseudomonas aeruginosa.
Authors: Wibowo, J.P. / Batista, F.A. / van Oosterwijk, N. / Groves, M.R. / Dekker, F.J. / Quax, W.J.
History
DepositionMay 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PvdP
B: PvdP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,1014
Polymers124,9162
Non-polymers1842
Water9,152508
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-26 kcal/mol
Surface area37990 Å2
Unit cell
Length a, b, c (Å)44.162, 112.616, 100.265
Angle α, β, γ (deg.)90.000, 92.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PvdP


Mass: 62458.223 Da / Num. of mol.: 2 / Fragment: PvdP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: pvdP, PA2392
Variant: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I188
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.27 % / Mosaicity: 0.16 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 3350, 0.1M Bis-Tris Propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2017 / Details: KB
RadiationMonochromator: Sir 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 55955 / % possible obs: 99.4 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.042 / Rrim(I) all: 0.091 / Net I/σ(I): 12.2
Reflection shell

Rmerge(I) obs: 0.657 / Num. unique obs: 4391 / CC1/2: 0.841 / Rpim(I) all: 0.339 / Rrim(I) all: 0.742 / Diffraction-ID: 1 / Redundancy: 4.5 % / Resolution: 2.11→2.17 Å

% possible all
95.7
95.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimless0.5.32data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.11→49.13 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.417 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2896 5.2 %RANDOM
Rwork0.169 ---
obs0.1717 53032 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.78 Å2 / Biso mean: 32.953 Å2 / Biso min: 17.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å20 Å2-0.53 Å2
2---0.4 Å20 Å2
3----1.87 Å2
Refinement stepCycle: final / Resolution: 2.11→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7631 0 12 508 8151
Biso mean--48.93 35.13 -
Num. residues----932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137898
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177123
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.64110728
X-RAY DIFFRACTIONr_angle_other_deg1.3881.5816402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0165923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9519.827521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.698151211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.631596
X-RAY DIFFRACTIONr_chiral_restr0.080.2907
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028961
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021971
LS refinement shellResolution: 2.11→2.164 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.293 203 -
Rwork0.301 3705 -
obs--94.79 %

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