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- PDB-6s7e: Plant Cysteine Oxidase PCO4 from Arabidopsis thaliana (using PEG ... -

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Basic information

Entry
Database: PDB / ID: 6s7e
TitlePlant Cysteine Oxidase PCO4 from Arabidopsis thaliana (using PEG 3350 and NaF as precipitants)
ComponentsPlant cysteine oxidase 4
KeywordsOXIDOREDUCTASE / double stranded beta helix fold / cysteine dioxygenase / iron cofactor / oxygen sensing
Function / homology
Function and homology information


peptidyl-cysteine oxidation / detection of hypoxia / cysteine dioxygenase / cysteine dioxygenase activity / cellular response to hypoxia / iron ion binding / nucleus / cytoplasm
Similarity search - Function
Cysteine oxygenase/2-aminoethanethiol dioxygenase / PCO_ADO / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
: / Plant cysteine oxidase 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWhite, M.D. / Levy, C.W. / Flashman, E. / McDonough, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structures of Arabidopsis thaliana oxygen-sensing plant cysteine oxidases 4 and 5 enable targeted manipulation of their activity.
Authors: White, M.D. / Dalle Carbonare, L. / Lavilla Puerta, M. / Iacopino, S. / Edwards, M. / Dunne, K. / Pires, E. / Levy, C. / McDonough, M.A. / Licausi, F. / Flashman, E.
History
DepositionJul 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Plant cysteine oxidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4452
Polymers29,3891
Non-polymers561
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-13 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.410, 71.710, 73.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Plant cysteine oxidase 4


Mass: 29389.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PCO4, At2g42670, F14N22.6 / Plasmid: pET 28A
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9SJI9, cysteine dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2M NaF, 45 mg/ml protein, 8mM RAP2.12 peptide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2018
RadiationMonochromator: double crystal Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.82→26.46 Å / Num. obs: 22349 / % possible obs: 99.1 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.034 / Rrim(I) all: 0.084 / Net I/σ(I): 12.1 / Num. measured all: 138901
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.82-1.876.51.7081027615930.6050.7211.8561.298
8.14-26.465.40.03915642920.9980.0180.04333.696.6

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→26.457 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.48
RfactorNum. reflection% reflection
Rfree0.2369 1256 5.63 %
Rwork0.1877 --
obs0.1903 22303 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.09 Å2 / Biso mean: 44.21 Å2 / Biso min: 23.57 Å2
Refinement stepCycle: final / Resolution: 1.82→26.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 1 148 1872
Biso mean--29.9 46.98 -
Num. residues----222
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8201-1.8930.33761540.3059224298
1.893-1.97910.28941430.2592227998
1.9791-2.08340.31411620.2243226798
2.0834-2.21390.24571350.2043231199
2.2139-2.38470.22471300.1952233099
2.3847-2.62450.29311400.1826232899
2.6245-3.00380.21411120.18192382100
3.0038-3.78270.20941410.17382396100
3.7827-26.4570.22241390.1772512100
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)
13.99844.4356-1.07967.132-0.043.8741-0.11980.24150.7023-0.5730.05251.0362-0.2754-0.23350.10440.37540.0758-0.15840.2959-0.02490.386312.358133.266812.0673
23.9401-2.42721.38534.2234-4.62387.4726-0.18930.05990.3353-0.73430.37380.6155-0.1453-0.5391-0.18640.3895-0.0158-0.09330.266-0.04220.363515.517441.137517.8173
36.8183-0.847-0.68699.5144-3.48529.57130.1705-0.7526-1.02920.25780.4531-0.06011.0838-0.0079-0.70340.5240.0458-0.05470.3558-0.02750.491824.821421.991128.8285
43.75640.89761.11596.920.93176.2828-0.20260.1673-0.1704-0.58930.1752-0.4219-0.01140.04670.04450.32480.0077-0.00030.2563-0.03680.306527.946432.167116.0502
51.93992.3360.01325.54650.69251.09740.1362-0.1616-0.01410.1332-0.0181-0.27420.15920.1825-0.11240.28330.0343-0.00960.2911-0.04170.29731.030739.782727.1035
64.71884.5194-1.73479.0763-2.25113.7779-0.05870.17970.1079-0.3130.1324-0.23580.220.29350.02860.30620.0436-0.04170.3956-0.03830.285435.823450.41229.353
72.16221.75620.49746.8088-0.12652.4480.1442-0.0121-0.1914-0.0492-0.1208-0.20350.23430.199-0.06440.23630.0221-0.03090.2311-0.0370.261327.17140.458426.1309
87.48424.63767.67825.70195.11219.113-0.1250.818-0.4657-0.54790.5784-0.7636-0.36011.0089-0.46310.37750.00050.09860.4774-0.07640.445842.474347.281522.9376
95.1888-3.7266-2.36079.15855.21513.12410.27750.08210.6493-0.2294-0.0534-0.792-0.2927-0.21-0.27170.35850.0102-0.00820.4934-0.0760.492240.968959.604332.0919
106.74064.47292.5773.99471.76471.9240.2327-0.0581-0.37180.09480.0343-0.83670.26870.2904-0.67610.43550.0165-0.01720.2861-0.06940.528931.894227.755317.8746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 16 )A-1 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 41 )A17 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 70 )A42 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 89 )A71 - 89
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 121 )A90 - 121
6X-RAY DIFFRACTION6chain 'A' and (resid 122 through 147 )A122 - 147
7X-RAY DIFFRACTION7chain 'A' and (resid 148 through 179 )A148 - 179
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 204 )A180 - 204
9X-RAY DIFFRACTION9chain 'A' and (resid 205 through 220 )A205 - 220
10X-RAY DIFFRACTION10chain 'A' and (resid 221 through 241 )A221 - 241

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