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- PDB-7cxz: crystal structure of pco2 -

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Basic information

Entry
Database: PDB / ID: 7cxz
Titlecrystal structure of pco2
ComponentsPlant cysteine oxidase 2
KeywordsPROTEIN BINDING / oxidase / metal binding / enzyme / metal binding protein
Function / homology
Function and homology information


peptidyl-cysteine oxidation / detection of hypoxia / cysteine dioxygenase / cysteine dioxygenase activity / cellular response to hypoxia / response to hypoxia / iron ion binding / nucleus / cytosol
Similarity search - Function
Cysteine oxygenase/2-aminoethanethiol dioxygenase / PCO_ADO / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / NICKEL (II) ION / Plant cysteine oxidase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.561 Å
AuthorsGuo, Q. / Xu, C. / Liao, S. / Chen, Z.
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Molecular basis for cysteine oxidation by plant cysteine oxidases from Arabidopsis thaliana.
Authors: Chen, Z. / Guo, Q. / Wu, G. / Wen, J. / Liao, S. / Xu, C.
History
DepositionSep 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Mar 31, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.3Nov 29, 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

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Assembly

Deposited unit
A: Plant cysteine oxidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2614
Polymers28,0241
Non-polymers2373
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.073, 46.820, 56.126
Angle α, β, γ (deg.)90.000, 100.940, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Plant cysteine oxidase 2


Mass: 28023.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PCO2, At5g39890, MYH19.8
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8LGJ5, 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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


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


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium acetate trihydrate, 0.1M Tris hydrochloride pH8.5, 30%w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 46618 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 31.9
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 8.6 / Num. unique obs: 1624 / CC1/2: 0.968 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CHI

7chi


Resolution: 1.561→25.143 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1854 2801 6.01 %
Rwork0.157 43817 -
obs0.1588 46618 72.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 44.1 Å2 / Biso mean: 16.9972 Å2 / Biso min: 6.97 Å2
Refinement stepCycle: final / Resolution: 1.561→25.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 10 263 2183
Biso mean--9.94 25.7 -
Num. residues----245
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.561-1.58760.2029960.1668149950
1.5876-1.61640.17471000.1629155351
1.6164-1.64750.18991010.164156851
1.6475-1.68110.24980.166153951
1.6811-1.71770.17521010.1714155351
1.7177-1.75760.1866990.1758153951
1.7576-1.80160.2219990.1871156451
1.8016-1.85030.18591060.1727160053
1.8503-1.90470.22521040.1741169555
1.9047-1.96620.20211210.161190863
1.9662-2.03640.1931430.1585221272
2.0364-2.11790.18061550.1592236378
2.1179-2.21420.18471670.1571268187
2.2142-2.33090.21251790.1622283493
2.3309-2.47680.1611840.161289096
2.4768-2.66790.19451900.1661296497
2.6679-2.9360.21271870.1608296597
2.936-3.35990.16521910.1501297098
3.3599-4.22990.17541900.1367290796
4.2299-25.1430.17281900.1537301399

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