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- PDB-6rrq: Crystal structure of tyrosinase PvdP from Pseudomonas aeruginosa ... -

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Basic information

Entry
Database: PDB / ID: 6rrq
TitleCrystal structure of tyrosinase PvdP from Pseudomonas aeruginosa bound to copper
ComponentsPvdP
KeywordsOXIDOREDUCTASE / tyrosinase / pyoverdine / copper
Function / homologytyrosinase activity / pyoverdine biosynthetic process / Di-copper centre-containing domain superfamily / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / metal ion binding / COPPER (II) ION / PvdP
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: PvdP
B: PvdP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,1107
Polymers124,7642
Non-polymers3465
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-79 kcal/mol
Surface area37560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.722, 114.215, 100.906
Angle α, β, γ (deg.)90.000, 94.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PvdP


Mass: 62382.105 Da / Num. of mol.: 2 / Fragment: PvdP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pvdP, PA2392 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I188
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.68 Å3/Da / Density % sol: 54.13 % / Mosaicity: 0.1 °
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: 2.7→49.66 Å / Num. obs: 31354 / % possible obs: 99.3 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.052 / Rrim(I) all: 0.102 / Net I/σ(I): 11.1
Reflection shell

Rmerge(I) obs: 0.552 / Num. unique obs: 4186 / CC1/2: 0.795 / Rpim(I) all: 0.339 / Rrim(I) all: 0.65 / Diffraction-ID: 1 / Redundancy: 3.6 % / % possible all: 99.1 / Resolution: 2.7→2.83 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.2data scaling
MOLREPphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RRR

6rrr


Resolution: 2.7→49.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.903 / SU B: 15.781 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.359
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2596 1654 5.3 %RANDOM
Rwork0.1856 ---
obs0.1897 29680 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 139.03 Å2 / Biso mean: 49.838 Å2 / Biso min: 15.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.02 Å2
2---0.09 Å20 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 2.7→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7317 0 10 131 7458
Biso mean--52.68 34.8 -
Num. residues----896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197571
X-RAY DIFFRACTIONr_bond_other_d0.0020.026801
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.93510282
X-RAY DIFFRACTIONr_angle_other_deg1.004315665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48922.118406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.215151165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4651590
X-RAY DIFFRACTIONr_chiral_restr0.0850.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021792
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 122 -
Rwork0.331 2195 -
all-2317 -
obs--98.93 %

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