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- PDB-6sbp: Plant Cysteine Oxidase PCO5 from Arabidopsis thaliana -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6sbp
TitlePlant Cysteine Oxidase PCO5 from Arabidopsis thaliana
ComponentsPlant cysteine oxidase 5
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
NICKEL (II) ION / Plant cysteine oxidase 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsWhite, M.D. / 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 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 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 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5773
Polymers29,4261
Non-polymers1512
Water1,802100
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-11 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.910, 68.910, 123.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-301-

GOL

21A-497-

HOH

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Components

#1: Protein Plant cysteine oxidase 5


Mass: 29426.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PCO5, At3g58670, T20N10.20 / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9LXT4, cysteine dioxygenase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M Ammonium nitrate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.9763
SYNCHROTRONDiamond I0221.0721
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELMar 7, 2016
DECTRIS PILATUS 6M-F2PIXELFeb 11, 2016
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystalSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
21.07211
Reflection

Entry-ID: 6SBP

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rrim(I) allDiffraction-IDNet I/σ(I)Biso Wilson estimate (Å2)Rmerge(I) obsRpim(I) all
1.91-48.74264413599.8312.810.065121
2.15-48.411691199.912.610.039232.761.6050.0350.011
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible allRmerge(I) obsRpim(I) all
1.91-1.9613.52.417200.81.2551100
2.15-2.2113.32.1163030.7571.478299.71.3780.403

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→48.727 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.42
RfactorNum. reflection% reflection
Rfree0.2188 2151 4.94 %
Rwork0.2048 --
obs0.2055 43502 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.72 Å2 / Biso mean: 62.9523 Å2 / Biso min: 32.85 Å2
Refinement stepCycle: final / Resolution: 1.91→48.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 7 101 1943
Biso mean--73.14 54.69 -
Num. residues----241
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.91-1.95450.6061230.6301224981
1.9545-2.00340.41021440.4144273497
2.0034-2.05750.36161440.30822798100
2.0575-2.11810.31561770.28622781100
2.1181-2.18640.30871510.27852785100
2.1864-2.26460.47391370.3814279899
2.2646-2.35520.321500.2933275799
2.3552-2.46240.23451370.23112817100
2.4624-2.59220.23951320.21862791100
2.5922-2.75460.20681480.20742813100
2.7546-2.96730.23231270.20612812100
2.9673-3.26590.22481490.20022807100
3.2659-3.73830.22151500.18112798100
3.7383-4.70920.12281290.14642811100
4.7092-48.7270.17621530.17622800100
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)
17.56233.65322.27831.88470.79941.45020.6539-0.54140.51310.3693-0.4976-0.39760.7810.6433-0.10770.9855-0.0765-0.08310.87950.01520.9747-39.2366-10.8558-2.7541
26.0625-0.42041.69493.787-0.40563.16580.2862-0.2601-0.3143-0.2073-0.06280.48250.318-0.5116-0.16290.3617-0.0572-0.09610.36630.07960.3823-15.3387.48644.8188
35.13670.63670.49648.2878-0.77375.54140.0592-1.36831.00271.435-0.12270.2592-0.6903-0.40640.04630.6469-0.0474-0.08290.8136-0.22540.61610.51717.788722.9973
45.29850.63622.0622.6677-0.93014.4150.1963-0.43710.24770.1025-0.05940.1279-0.0102-0.3287-0.11750.3557-0.0105-0.06470.39570.03160.3838-8.857510.59368.9926
54.29410.60422.43541.70950.06633.54680.02390.48910.4831-0.01170.02940.104-0.18370.4652-0.12540.4465-0.0302-0.01470.3761-0.07520.5164-2.403317.971211.0513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -11 through 3 )A-11 - 3
2X-RAY DIFFRACTION2chain 'A' and (resid 4 through 119 )A4 - 119
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 140 )A120 - 140
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 192 )A141 - 192
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 242 )A193 - 242

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