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- PDB-6s0p: Plant Cysteine Oxidase PCO4 from Arabidopsis thaliana -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6s0p
TitlePlant Cysteine Oxidase PCO4 from Arabidopsis thaliana
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: 1.24 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
DepositionJun 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 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
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-15 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.712, 68.994, 71.306
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: obtained synthetically / Details: N-terminal 6-His tag / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SJI9, cysteine dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


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


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.98 Å3/Da / Density % sol: 38.02 % / Description: triangular plate
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.18 to 2.3M (NH4)2SO4 and 0.10 M TrisHCl, protein concentration of 45 mg/mL
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2017 / Details: CRL
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.24→68.98 Å / Num. obs: 61822 / % possible obs: 100 % / Redundancy: 12 % / Biso Wilson estimate: 15.715 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Net I/σ(I): 12.7
Reflection shell

Rpim(I) all: 0.497 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.24-1.2611.61.6130.930200.8531.691100
3.37-68.9811.90.03658.833300.9990.037100

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Processing

Software
NameVersionClassification
DIALS1.5.0-gbc51d76c-hotfix1data reduction
Aimless0.5.31data scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→37.267 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26
RfactorNum. reflection% reflection
Rfree0.2089 5939 5.12 %
Rwork0.1789 --
obs0.1804 115968 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.49 Å2 / Biso mean: 26.8751 Å2 / Biso min: 11.15 Å2
Refinement stepCycle: final / Resolution: 1.24→37.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 1 188 1895
Biso mean--14.33 35.24 -
Num. residues----219
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2402-1.25430.39171980.3733591378996
1.2543-1.2690.34751800.36563549372995
1.269-1.28450.37611790.34953620379996
1.2845-1.30080.32081790.33213604378397
1.3008-1.31790.33092030.30553690389399
1.3179-1.33590.30451970.29383714391199
1.3359-1.3550.3291890.29643769395899
1.355-1.37530.33472200.29613668388899
1.3753-1.39680.29052470.256736533900100
1.3968-1.41970.28722400.255536863926100
1.4197-1.44410.31092370.246136783915100
1.4441-1.47040.30151950.238437213916100
1.4704-1.49870.25471690.228737943963100
1.4987-1.52930.25421420.209937503892100
1.5293-1.56250.2621740.19063752392699
1.5625-1.59890.26792210.19343654387599
1.5989-1.63890.23871660.18913726389298
1.6389-1.68320.23481880.19233685387398
1.6832-1.73270.24562480.19563558380697
1.7327-1.78860.22361820.19073611379396
1.7886-1.85250.23832110.18693576378797
1.8525-1.92670.18791710.16813668383998
1.9267-2.01440.1852240.14083663388799
2.0144-2.12060.18472050.1433652385798
2.1206-2.25340.20722210.14943597381897
2.2534-2.42740.14911960.15073575377196
2.4274-2.67160.1751440.16053673381798
2.6716-3.0580.20112040.16083716392099
3.058-3.85220.15272070.14733709391699
3.8522-37.28340.19642020.164737273929100

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