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- PDB-6im8: CueO-PM2 multicopper oxidase -

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Basic information

Entry
Database: PDB / ID: 6im8
TitleCueO-PM2 multicopper oxidase
ComponentsBlue copper oxidase CueO,PM2 peptide,Blue copper oxidase CueO
KeywordsOXIDOREDUCTASE / Multicopper oxidase / Laccase
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / oxidoreductase activity, acting on metal ions / detoxification of copper ion / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to copper ion / ferroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Multicopper oxidase CueO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsWongsantichon, J. / Robinson, R. / Ghadessy, F.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Singapore
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Development and structural characterization of an engineered multi-copper oxidase reporter of protein-protein interactions.
Authors: Sana, B. / Chee, S.M.Q. / Wongsantichon, J. / Raghavan, S. / Robinson, R.C. / Ghadessy, F.J.
History
DepositionOct 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Blue copper oxidase CueO,PM2 peptide,Blue copper oxidase CueO


Theoretical massNumber of molelcules
Total (without water)55,8471
Polymers55,8471
Non-polymers00
Water9,170509
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17630 Å2
Unit cell
Length a, b, c (Å)50.343, 90.961, 60.425
Angle α, β, γ (deg.)90.000, 104.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Blue copper oxidase CueO,PM2 peptide,Blue copper oxidase CueO / Copper efflux oxidase


Mass: 55846.766 Da / Num. of mol.: 1 / Mutation: M358I
Source method: isolated from a genetically manipulated source
Details: Chimera protein CueO-PM2 multicopper oxidase
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) synthetic construct (others)
Strain: K12 / Gene: cueO, yacK, b0123, JW0119 / Production host: Escherichia coli (E. coli) / References: UniProt: P36649
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 18% w/v Polyethylene glycol 4000, 10% w/v 2-Propanol, 100mM Tris pH 8, 200mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 47465 / % possible obs: 97.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.92 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.043 / Rrim(I) all: 0.081 / Χ2: 5.129 / Net I/σ(I): 18.2 / Num. measured all: 171001
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.833.70.13524170.9790.0820.1581.1299.9
1.83-1.863.70.13423970.9810.0810.1571.33299.5
1.86-1.93.60.15623200.9740.0940.1822.40496.5
1.9-1.942.90.31321470.8320.1920.36824.41587
1.94-1.983.60.15523590.9640.0940.1824.85798.8
1.98-2.033.70.124290.9860.0590.1162.27699.8
2.03-2.083.70.12123950.9770.0730.1414.95599.6
2.08-2.133.70.09424090.9860.0570.112.76999.6
2.13-2.23.70.08624460.9880.0510.12.858100
2.2-2.273.10.20321890.8350.1320.24316.71389.8
2.27-2.353.60.0823500.9910.0480.0933.0897.5
2.35-2.443.80.07524300.9920.0450.0873.321100
2.44-2.553.80.07224180.9910.0430.0843.277100
2.55-2.693.80.07224320.9920.0430.0833.811100
2.69-2.863.70.06524390.9920.0390.0763.707100
2.86-3.083.80.06424280.9930.0380.0744.26799.9
3.08-3.393.70.06424370.9920.0390.0755.24299.1
3.39-3.883.20.06622930.9890.0420.0798.96994.2
3.88-4.883.50.04422550.9950.0280.0523.86891.9
4.88-503.70.03924750.9940.0240.04610.12598.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KV7

1kv7


Resolution: 1.801→35.881 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.72
RfactorNum. reflection% reflection
Rfree0.1941 2328 4.94 %
Rwork0.1608 --
obs0.1624 47096 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.38 Å2 / Biso mean: 26.9263 Å2 / Biso min: 10.01 Å2
Refinement stepCycle: final / Resolution: 1.801→35.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 0 509 4113
Biso mean---36.93 -
Num. residues----469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8009-1.83770.24751360.18852682281899
1.8377-1.87770.23331540.19152671282599
1.8777-1.92130.39251160.33942329244586
1.9213-1.96940.32021450.25592422256790
1.9694-2.02260.20761480.169227302878100
2.0226-2.08210.20161220.1532694281699
2.0821-2.14930.21291430.156927092852100
2.1493-2.22610.19691470.15742644279198
2.2261-2.31530.2521190.22752401252088
2.3153-2.42060.2161330.15927292862100
2.4206-2.54820.20371300.165627182848100
2.5482-2.70780.22841390.162927182857100
2.7078-2.91680.19021270.160127272854100
2.9168-3.21010.18821510.15527242875100
3.2101-3.67430.17191610.14662656281798
3.6743-4.62760.1491100.11972465257590
4.6276-35.88810.13581470.13072749289699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71750.36850.21381.2327-0.00070.6363-0.040.15930.05390.0729-0.00770.20710.0278-0.12010.04070.16910.0197-0.01960.2449-0.02840.219-5.2906-0.00268.6458
21.4264-0.1666-0.22671.3497-0.05421.4049-0.01760.0299-0.05050.0768-0.02330.23340.0312-0.19620.0350.1129-0.0034-0.00150.1788-0.01880.2118-9.6243-9.475469.0911
31.41160.5169-0.2132.0769-0.03341.45990.0435-0.0506-0.13680.2654-0.038-0.40130.06470.0805-0.01270.1380.0141-0.05670.14550.01760.190818.6957-11.394677.7415
40.90290.1516-0.02121.0877-0.14170.5048-0.0076-0.0102-0.03270.0588-0.0194-0.03450.0330.00390.02860.12490.0038-0.0130.1314-0.0040.12949.3503-8.593571.0956
51.4515-0.334-0.09011.39930.24061.08730.0310.04480.2587-0.0181-0.0384-0.068-0.14650.0588-0.00230.1461-0.0043-0.0130.12330.01930.162111.26957.525666.4955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 323 through 376 )A323 - 376
2X-RAY DIFFRACTION2chain 'A' and (resid 377 through 519 )A377 - 519
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 69 )A29 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 267 )A70 - 267
5X-RAY DIFFRACTION5chain 'A' and (resid 268 through 322 )A268 - 322

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