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- PDB-5k21: Pyocyanin demethylase -

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Basic information

Entry
Database: PDB / ID: 5k21
TitlePyocyanin demethylase
ComponentsPyocyanin demethylase
KeywordsOXIDOREDUCTASE / Demethylase Phenazine
Function / homologyAllene oxide cyclase/Dirigent protein / membrane => GO:0016020 / metal ion binding / phenazin-1-ol / Uncharacterized protein
Function and homology information
Biological speciesMycobacterium fortuitum subsp. fortuitum DSM 46621 = ATCC 6841 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCosta, K.C. / Glasser, N.R. / Newman, D.K.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32AI112248 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5R01HL117328-03 United States
CitationJournal: Science / Year: 2017
Title: Pyocyanin degradation by a tautomerizing demethylase inhibits Pseudomonas aeruginosa biofilms.
Authors: Costa, K.C. / Glasser, N.R. / Conway, S.J. / Newman, D.K.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyocyanin demethylase
B: Pyocyanin demethylase
C: Pyocyanin demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3789
Polymers45,6693
Non-polymers7096
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-33 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.330, 72.980, 79.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pyocyanin demethylase


Mass: 15222.981 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium fortuitum subsp. fortuitum DSM 46621 = ATCC 6841 (bacteria)
Gene: MFORT_14352 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K0V2D8
#2: Chemical ChemComp-6QF / phenazin-1-ol / 1-hydroxyphenazine


Mass: 196.205 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H8N2O
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.08 Å3/Da / Density % sol: 40.87 %
Description: Rods with dimensions of 50 x 50 x 100 micrometers
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 8000, 200 mM NaCl, 200 micromolar 1-hydroxyphenazine, 1% DMSO, and 100 mM sodium phosphate dibasic/citric acid, pH 4.2 mixed 1:1 with 5 mg/mL protein in 20 mM Tris, pH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03318 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 1.8→34.98 Å / Num. obs: 35992 / % possible obs: 99.98 % / Redundancy: 25.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1765 / Net I/σ(I): 13.29

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
XDSdata scaling
XSCALEdata scaling
PHENIXmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.98 Å / Cross valid method: FREE R-VALUE
Details: TLS groups generated by phenix.refine. Hydrogens in their riding positions.
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 3644 10.1 %Random
Rwork0.1679 ---
obs-35987 99.98 %-
Displacement parametersBiso mean: 36.53 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 48 213 2905

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