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- PDB-6lyx: Crystal structure of oxidized ACHT1 -

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Basic information

Entry
Database: PDB / ID: 6lyx
TitleCrystal structure of oxidized ACHT1
ComponentsThioredoxin-like 2-1, chloroplastic
KeywordsOXIDOREDUCTASE / Arabidopsis thaliana / 2-Cys PrxA / Peroxidase activity.
Function / homology
Function and homology information


regulation of photosynthesis / detection of redox state / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / chloroplast stroma / chloroplast / cell redox homeostasis
Similarity search - Function
Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin-like 2-1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.696 Å
AuthorsWang, J.C. / Pan, W.M. / Cai, W.G. / Wang, M.Z. / Zhang, M.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural insight into the biological functions of Arabidopsis thaliana ACHT1.
Authors: Wang, J. / Pan, W. / Cai, W. / Wang, M. / Liu, L. / Zhang, M.
History
DepositionFeb 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 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: Thioredoxin-like 2-1, chloroplastic
B: Thioredoxin-like 2-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8684
Polymers34,6802
Non-polymers1882
Water5,873326
1
A: Thioredoxin-like 2-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5283
Polymers17,3401
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area6460 Å2
MethodPISA
2
B: Thioredoxin-like 2-1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)17,3401
Polymers17,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.611, 102.537, 92.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

21A-552-

HOH

31B-425-

HOH

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Components

#1: Protein Thioredoxin-like 2-1, chloroplastic / Atypical cysteine/histidine-rich thioredoxin 1 / AtACHT1


Mass: 17339.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g26160, F20B18.270 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8LEK4
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: ammonium sulfate, isopropanol,agarose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 52914 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 14.19 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Χ2: 0.936 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.765.50.6952040.8460.320.7630.78199.6
1.76-1.837.30.50452530.940.20.5430.817100
1.83-1.917.40.33452070.9720.1320.360.911100
1.91-2.027.40.23152740.9840.0910.2490.983100
2.02-2.147.40.1752550.9880.0670.1831.07100
2.14-2.317.40.12752810.9920.050.1361.071100
2.31-2.547.30.10552620.9940.0420.1131.02100
2.54-2.917.30.08853140.9940.0350.0950.963100
2.91-3.666.70.07353490.9950.0320.080.96100
3.66-506.50.06255150.9950.0270.0680.72399.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.25data extraction
ARP/wARPdata processing
AMBERrefinement
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zzx

3zzx


Resolution: 1.696→38.93 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.29
RfactorNum. reflection% reflection
Rfree0.1887 2457 4.8 %
Rwork0.1734 --
obs0.1741 51212 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.5 Å2 / Biso mean: 18.41 Å2 / Biso min: 3.6 Å2
Refinement stepCycle: final / Resolution: 1.696→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 11 326 2243
Biso mean--21.78 34.11 -
Num. residues----239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072000
X-RAY DIFFRACTIONf_angle_d1.0252702
X-RAY DIFFRACTIONf_chiral_restr0.081283
X-RAY DIFFRACTIONf_plane_restr0.004346
X-RAY DIFFRACTIONf_dihedral_angle_d10.653733
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.696-1.72860.2104780.2219129647
1.7286-1.76390.25941080.2157236285
1.7639-1.80230.23291540.2094275699
1.8023-1.84420.18961430.18352779100
1.8442-1.89030.19931400.17312790100
1.8903-1.94140.18731280.17712817100
1.9414-1.99850.21961390.16942776100
1.9985-2.0630.16371290.15352810100
2.063-2.13680.16471490.15942799100
2.1368-2.22230.18771470.15512785100
2.2223-2.32350.16771350.16012809100
2.3235-2.44590.18621480.16782807100
2.4459-2.59910.18831310.16772824100
2.5991-2.79980.20411420.17582834100
2.7998-3.08140.15761370.172826100
3.0814-3.52710.21141610.17122832100
3.5271-4.44270.16121570.15542864100
4.4427-38.930.21281310.2032298999
Refinement TLS params.Method: refined / Origin x: 19.1816 Å / Origin y: 63.0548 Å / Origin z: 16.02 Å
111213212223313233
T0.0378 Å2-0.0004 Å20.0057 Å2-0.047 Å2-0.0044 Å2--0.0475 Å2
L0.0707 °2-0.1674 °2-0.1073 °2-0.3038 °20.2337 °2--0.2285 °2
S-0.0109 Å °-0.0297 Å °-0.0147 Å °0.0011 Å °0.0146 Å °0.0187 Å °-0.0054 Å °0.0353 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA85 - 241
2X-RAY DIFFRACTION1allB84 - 205
3X-RAY DIFFRACTION1allB240
4X-RAY DIFFRACTION1allS1 - 326

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