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- PDB-7chj: crystal structure of pco4 -

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Basic information

Entry
Database: PDB / ID: 7chj
Titlecrystal structure of pco4
ComponentsPlant cysteine oxidase 4
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 / RmlC-like jelly roll fold
Similarity search - Domain/homology
CITRIC ACID / : / Plant cysteine oxidase 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 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 1.3Mar 27, 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
B: Plant cysteine oxidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1305
Polymers54,8262
Non-polymers3043
Water1,69394
1
A: Plant cysteine oxidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4692
Polymers27,4131
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-13 kcal/mol
Surface area12190 Å2
MethodPISA
2
B: Plant cysteine oxidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6613
Polymers27,4131
Non-polymers2482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-13 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.618, 51.701, 82.064
Angle α, β, γ (deg.)90.000, 108.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Plant cysteine oxidase 4


Mass: 27413.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PCO4, At2g42670, F14N22.6
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.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 3350, 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate pH5.0

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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: 2.44→50 Å / Num. obs: 26972 / % possible obs: 99.2 % / Redundancy: 6.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.119 / Net I/σ(I): 14.2
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 4 / Num. unique obs: 1580 / CC1/2: 0.941

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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 / Resolution: 2.44→31.141 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 2694 10 %
Rwork0.2054 24258 -
obs0.2114 26952 81.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.68 Å2 / Biso mean: 40.2225 Å2 / Biso min: 15.98 Å2
Refinement stepCycle: final / Resolution: 2.44→31.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 0 15 94 3634
Biso mean--52.82 33.53 -
Num. residues----451
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.44-2.4840.3521770.302869044
2.484-2.53180.3626900.271878151
2.5318-2.58340.31091000.284888456
2.5834-2.63960.31321060.266298663
2.6396-2.70090.349980.26111969
2.7009-2.76840.33171360.2644109273
2.7684-2.84320.37931440.2601120376
2.8432-2.92680.25541340.2413124180
2.9268-3.02120.28481470.2403131083
3.0212-3.12910.33221360.2305134585
3.1291-3.25430.25451660.2436138690
3.2543-3.40220.27651540.2178145393
3.4022-3.58130.28411690.2094151496
3.5813-3.80530.29271660.1922152398
3.8053-4.09860.25381750.1934153499
4.0986-4.50990.22951730.16471564100
4.5099-5.160.20541700.15641584100
5.16-6.49130.24121690.18961540100
6.4913-31.140.22721840.179150998
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)
11.14950.32961.46325.0283-2.25744.8932-0.33030.31770.1516-1.19740.23510.42820.1277-0.1649-0.06590.5323-0.1027-0.10570.37860.02150.4066-10.8725-25.8298-37.6646
2-0.03610.48980.62353.60270.17492.5691-0.58540.33680.0392-0.75980.56540.3678-0.48540.22540.01930.17910.0579-0.020.24360.0530.2329-11.44612.8388-14.3186
33.03611.7026-0.76883.75572.52516.56810.3045-0.3058-0.21780.2517-0.19180.51710.2703-0.01090.06890.25880.012-0.01280.28330.08620.3132-9.0880.7814-14.8856
46.13940.29060.42733.49731.36551.19270.09810.06640.03980.446-0.5850.60920.0281-0.00460.19410.2758-0.03690.00350.2707-0.00720.2104-12.046715.83813.4912
51.37481.05321.7023.4035-2.93944.7206-0.10520.02620.24770.55390.05210.7175-0.381-0.73840.16250.25850.04280.07690.293-0.05320.316-20.64966.5305-4.2127
6-0.541-0.5451.87773.3651-0.05820.3534-0.1221-0.00170.03360.5957-0.2174-0.01920.22410.16590.18410.2508-0.08330.02010.2646-0.01130.2588-13.4589-2.87853.2159
71.1835-0.6401-1.09832.42471.30952.6198-0.60730.0176-0.546-0.16370.3656-0.1288-0.1903-0.25690.18210.25930.0409-0.0730.35150.10220.376-16.5043-17.74783.5383
8-0.06890.3132-1.42673.0197-2.06391.2835-0.13870.0939-0.15690.38780.05230.03340.0709-0.34720.11110.2044-0.0191-0.01440.3081-0.00960.3382-16.256-2.9331-1.9127
95.9478-2.52840.44469.2312-0.32322.0767-0.3524-0.5289-0.48781.28480.30390.44560.1375-0.0109-0.01820.3212-0.0633-0.00940.26510.05030.2814-12.8975-22.69268.1605
101.7061-0.5911-0.95515.7915-1.98563.62820.30980.1652-0.19450.94840.07071.1276-0.5749-0.4102-0.47740.3910.01970.10120.3809-0.07240.5276-23.68537.23631.3069
112.952-0.4727-1.04133.38930.95151.956-0.2931-0.5767-0.6069-0.02660.15780.1346-0.11730.18550.16030.291-0.03680.03240.29480.06630.2912-8.6346-30.0616-18.0696
122.5246-3.6645-1.60758.17041.74894.9606-0.2704-0.11890.08420.62610.3590.15840.1629-0.0933-0.02710.2992-0.0132-0.00450.31610.00980.37-5.7006-18.9975-15.9894
132.4376-0.1689-0.09654.4656-1.01981.3672-0.13510.1493-0.1731-0.82020.03030.13650.1772-0.05310.04480.4335-0.0128-0.02170.294-0.03020.231-6.119-29.0231-32.2377
141.96740.0804-0.37743.67940.19230.50180.14090.0758-0.0396-0.7224-0.0758-0.0362-0.02490.0751-0.04040.4019-0.00140.05240.297-0.00160.2256-0.962-15.5922-34.1007
152.167-0.0244-0.1463.9874-0.21252.0027-0.30720.0914-0.4794-0.08550.18340.2235-0.4143-0.1189-0.13930.3457-0.0403-0.06360.4280.04870.4961-3.5358-0.7011-36.0488
161.12160.66790.46571.9793-0.83971.2255-0.13570.00920.0073-0.26970.1002-0.20190.19490.047-0.01820.3376-0.01190.06650.2740.0480.289-0.6665-17.0571-30.2023
174.05862.1976-0.04294.9763-2.1384.84420.63481.06540.0285-0.6433-0.0411.1511-0.6077-1.5929-0.10940.60280.1358-0.09250.5218-0.11590.3824-16.7813-12.1867-33.2097
184.70581.4402-1.88898.10850.86021.8141-0.46130.13970.1248-0.98050.4321-0.547-0.21430.24950.09310.41020.04120.02660.36040.05640.35321.79284.1202-37.499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 221 through 241 )B221 - 241
2X-RAY DIFFRACTION2chain 'A' and (resid 0 through 15 )A0 - 15
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 36 )A16 - 36
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 70 )A37 - 70
5X-RAY DIFFRACTION5chain 'A' and (resid 71 through 89 )A71 - 89
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 121 )A90 - 121
7X-RAY DIFFRACTION7chain 'A' and (resid 122 through 147 )A122 - 147
8X-RAY DIFFRACTION8chain 'A' and (resid 148 through 192 )A148 - 192
9X-RAY DIFFRACTION9chain 'A' and (resid 193 through 220 )A193 - 220
10X-RAY DIFFRACTION10chain 'A' and (resid 221 through 241 )A221 - 241
11X-RAY DIFFRACTION11chain 'B' and (resid -1 through 16 )B-1 - 16
12X-RAY DIFFRACTION12chain 'B' and (resid 17 through 36 )B17 - 36
13X-RAY DIFFRACTION13chain 'B' and (resid 37 through 89 )B37 - 89
14X-RAY DIFFRACTION14chain 'B' and (resid 90 through 121 )B90 - 121
15X-RAY DIFFRACTION15chain 'B' and (resid 122 through 147 )B122 - 147
16X-RAY DIFFRACTION16chain 'B' and (resid 148 through 179 )B148 - 179
17X-RAY DIFFRACTION17chain 'B' and (resid 180 through 192 )B180 - 192
18X-RAY DIFFRACTION18chain 'B' and (resid 193 through 220 )B193 - 220

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