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- PDB-5yry: Crystal structure of C-terminal redox domain of APR1 from Arabido... -

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Basic information

Entry
Database: PDB / ID: 5yry
TitleCrystal structure of C-terminal redox domain of APR1 from Arabidopsis thaliana
Components5'-adenylylsulfate reductase 1, chloroplastic
KeywordsOXIDOREDUCTASE / Redox domain / Sulfer assimilatory / APS reductase
Function / homology
Function and homology information


adenylyl-sulfate reductase (glutathione) / adenylyl-sulfate reductase (glutathione) activity / adenylyl-sulfate reductase activity / : / sulfate assimilation / cysteine biosynthetic process / plastid / chloroplast stroma / chloroplast / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Thioredoxin-independent 5'-adenylylsulphate reductase / Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase family / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Rossmann-like alpha/beta/alpha sandwich fold / Thioredoxin-like superfamily
Similarity search - Domain/homology
5'-adenylylsulfate reductase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.698 Å
AuthorsHsu, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (Taiwan)NSC102-2113-M-002-005 Taiwan
CitationJournal: Antioxidants (Basel) / Year: 2019
Title: C-terminal Redox Domain ofArabidopsisAPR1 is a Non-Canonical Thioredoxin Domain with Glutaredoxin Function.
Authors: Chen, F.F. / Chien, C.Y. / Cho, C.C. / Chang, Y.Y. / Hsu, C.H.
History
DepositionNov 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _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: 5'-adenylylsulfate reductase 1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)14,1321
Polymers14,1321
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomeric form
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6630 Å2
Unit cell
Length a, b, c (Å)58.200, 58.200, 86.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 5'-adenylylsulfate reductase 1, chloroplastic / 3'-phosphoadenosine-5'-phosphosulfate reductase homolog 19 / Prh-19 / Adenosine 5'-phosphosulfate ...3'-phosphoadenosine-5'-phosphosulfate reductase homolog 19 / Prh-19 / Adenosine 5'-phosphosulfate 5'-adenylylsulfate sulfotransferase 1 / APS sulfotransferase 1 / Thioredoxin-independent APS reductase 1


Mass: 14132.117 Da / Num. of mol.: 1 / Fragment: C-terminal redox domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: APR1, PRH19, At4g04610, F4H6.13 / Production host: Escherichia coli (E. coli)
References: UniProt: P92979, adenylyl-sulfate reductase (glutathione)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Tris buffer pH 7.0, 1.2 M sodium citrate, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.698→24.16 Å / Num. obs: 4467 / % possible obs: 99.6 % / Redundancy: 12.9 % / Biso Wilson estimate: 61.11 Å2 / Rrim(I) all: 0.079 / Net I/σ(I): 32.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 4.7 / Num. unique obs: 432 / Rrim(I) all: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.698→24.16 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26
RfactorNum. reflection% reflection
Rfree0.2504 444 10.02 %
Rwork0.1793 --
obs0.1863 4433 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.698→24.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 0 1 935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008956
X-RAY DIFFRACTIONf_angle_d1.1941289
X-RAY DIFFRACTIONf_dihedral_angle_d18.192367
X-RAY DIFFRACTIONf_chiral_restr0.049138
X-RAY DIFFRACTIONf_plane_restr0.008166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6983-3.08810.31291430.2351283X-RAY DIFFRACTION99
3.0881-3.88810.2941460.20421316X-RAY DIFFRACTION100
3.8881-24.16090.2171550.15561390X-RAY DIFFRACTION100
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)
16.26123.16730.61193.34023.69546.25040.10690.8063-0.1766-1.490.50790.65970.36791.047-0.29720.95790.070.07870.8556-0.01390.1486-1.1854-19.9752-14.74
25.21496.21820.0857.4749-0.25962.05110.25830.57282.2849-1.66830.36311.9810.7445-0.5416-0.60030.84870.0156-0.16121.11430.07470.8337-16.6904-16.2283-16.2628
30.1152-0.3006-0.16481.8258-1.13766.7007-0.5411-0.00480.15580.2797-0.014-1.1228-0.86141.1288-0.79020.67360.07110.02860.8427-0.1595-0.20181.5608-18.9179-7.2422
46.31282.88616.03242.80954.18077.12531.1941-0.8126-1.51720.6523-0.622-0.48750.8085-0.4276-0.40730.84180.0247-0.0640.80760.02650.3243-1.0149-26.6679-1.3189
55.41982.0772-1.59873.672-1.81597.28390.50540.4801-0.2082-0.24310.02250.0345-0.2704-0.0857-0.40760.67790.041-0.00120.6768-0.01510.274-4.0542-21.8777-10.7113
62.00751.281-4.90292.44292.92827.43210.27590.51612.362-1.0805-0.4552-0.2703-2.71351.17040.19671.3666-0.1827-0.06590.86930.27780.52234.0657-7.4466-11.7201
77.0387-1.2547-3.29945.25550.24195.0725-0.6879-0.74121.51040.18680.4051-0.3364-1.49410.470.05150.76570.1073-0.11810.6719-0.17130.378-2.3775-13.0257-4.9884
86.69220.4557-6.15663.67462.32357.8434-2.47951.3951.4783-1.55571.89421.8703-3.17480.85581.06561.31570.0284-0.33991.0308-0.01680.7182-15.1921-10.6486-9.7116
96.22981.5084-1.21597.65940.13812.95170.101-1.21340.2350.4438-0.4647-0.03840.10990.4790.08570.6978-0.04850.07770.7814-0.03360.2205-6.1157-15.46731.4009
104.5616-4.42383.29149.342-1.99429.01270.7418-1.8072-1.2261.9332-0.27721.52380.7347-1.7073-0.69020.9278-0.1930.00461.16590.01520.3322-12.4596-24.40893.0265
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 23 )
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 33 )
4X-RAY DIFFRACTION4chain 'A' and (resid 34 through 50 )
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 63 )
6X-RAY DIFFRACTION6chain 'A' and (resid 64 through 73 )
7X-RAY DIFFRACTION7chain 'A' and (resid 74 through 85 )
8X-RAY DIFFRACTION8chain 'A' and (resid 86 through 92 )
9X-RAY DIFFRACTION9chain 'A' and (resid 93 through 98 )
10X-RAY DIFFRACTION10chain 'A' and (resid 99 through 112 )

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