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- PDB-7chi: crystal structure of pco5 -

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Basic information

Entry
Database: PDB / ID: 7chi
Titlecrystal structure of pco5
ComponentsPlant cysteine oxidase 5
KeywordsMETAL BINDING PROTEIN / oxidase / metal binding / enzyme
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 / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Plant cysteine oxidase 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.502 Å
AuthorsGuo, Q. / Xu, C. / Liao, S.
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
DepositionJul 5, 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 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plant cysteine oxidase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8342
Polymers27,7791
Non-polymers561
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-13 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.720, 67.720, 128.324
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-456-

HOH

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Components

#1: Protein Plant cysteine oxidase 5


Mass: 27778.576 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: PCO5, At3g58670, T20N10.20
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9LXT4, 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.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, sitting drop / Details: 12% PEG20000, 0.1M MES monohydrate pH 6.5

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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: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19655 / % possible obs: 100 % / Redundancy: 24.4 % / CC1/2: 0.985 / Rmerge(I) obs: 0.135 / Net I/σ(I): 32.6
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 1.625 / Mean I/σ(I) obs: 4 / Num. unique obs: 1064 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.502→24.717 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2262 1952 9.93 %
Rwork0.1798 17698 -
obs0.1845 19650 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.57 Å2 / Biso mean: 43.3026 Å2 / Biso min: 14.18 Å2
Refinement stepCycle: final / Resolution: 2.502→24.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 1 62 1761
Biso mean--17.31 42.44 -
Num. residues----220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5024-2.56490.30151360.25011252
2.5649-2.63420.35691380.23211269
2.6342-2.71160.25641400.22341284
2.7116-2.7990.22621420.20971245
2.799-2.89890.28351390.20781270
2.8989-3.01480.24331420.19821269
3.0148-3.15170.29231410.19531255
3.1517-3.31750.22951390.20531256
3.3175-3.52480.23251430.18971268
3.5248-3.79610.24441440.16251273
3.7961-4.17640.18831340.15811256
4.1764-4.7770.16171360.13041266
4.777-6.00420.18671380.15651272
6.0042-24.7170.21941400.18221263
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)
11.02930.1453-0.29951.45540.09190.32230.03660.04350.0338-0.1639-0.1249-0.3339-0.11950.18940.00060.2537-0.00430.06350.2798-0.00480.301953.597927.62544.4627
21.13310.0279-0.25450.97290.46940.68960.1086-0.0728-0.09780.0909-0.09150.00540.0475-0.0176-0.00030.2099-0.01090.04690.1527-0.00050.165440.623222.04259.4766
30.8954-0.31570.24190.530.02760.96850.15140.3602-0.28670.04280.0098-0.05350.2543-0.30190.05710.3145-0.0350.14770.17730.03470.323536.941916.149710.519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 89 )A2 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 192 )A90 - 192
3X-RAY DIFFRACTION3chain 'A' and (resid 193 through 242 )A193 - 242

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