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- PDB-8f9y: SAL1 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 8f9y
TitleSAL1 from Arabidopsis thaliana
ComponentsSAL1 phosphatase
KeywordsHYDROLASE / SAL1
Function / homology
Function and homology information


inositol-1,4-bisphosphate 1-phosphatase / inositol-1,4-bisphosphate 1-phosphatase activity / 3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / sulfate assimilation / abscisic acid-activated signaling pathway / metal ion binding
Similarity search - Function
3(2),5 -bisphosphate nucleotidase HAL2 / : / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family
Similarity search - Domain/homology
PHOSPHATE ION / 3'(2'),5'-bisphosphate nucleotidase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFrkic, R.L. / Kaczmarski, J.A. / Tan, L. / Jackson, C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Sensing and signaling of oxidative stress in chloroplasts by inactivation of the SAL1 phosphoadenosine phosphatase.
Authors: Chan, K.X. / Mabbitt, P.D. / Phua, S.Y. / Mueller, J.W. / Nisar, N. / Gigolashvili, T. / Stroeher, E. / Grassl, J. / Arlt, W. / Estavillo, G.M. / Jackson, C.J. / Pogson, B.J.
History
DepositionNov 24, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionJan 18, 2023ID: 5ESY
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAL1 phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7084
Polymers37,4941
Non-polymers2143
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.971, 142.971, 75.135
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein SAL1 phosphatase


Mass: 37494.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SAL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q42546
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20 to 30 % PEG 2000 MME, 0.2 M (NH4)2SO4, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→39.72 Å / Num. obs: 14420 / % possible obs: 100 % / Redundancy: 78.2 % / Biso Wilson estimate: 89.91 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.022 / Rrim(I) all: 0.196 / Net I/σ(I): 29.5 / Num. measured all: 1128236 / Scaling rejects: 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.6-2.7281.39.917080.3651.68215.261100
9.01-39.7258.90.03241510.0040.03399

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→39.72 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 714 4.96 %
Rwork0.2082 13670 -
obs0.2104 14384 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 444.76 Å2 / Biso mean: 128.4161 Å2 / Biso min: 51.53 Å2
Refinement stepCycle: final / Resolution: 2.6→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 11 10 2649
Biso mean--146.69 117.99 -
Num. residues----352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.80.3991400.363726572797
2.8-3.080.41291520.339826642816
3.08-3.530.33711380.275827022840
3.53-4.440.24191320.206827552887
4.44-39.720.21191520.167128923044
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)
15.5878-1.94830.88046.50291.02725.5794-0.00150.83160.1067-1.1326-0.34850.8319-0.4861-0.4840.3710.8230.022-0.12020.79310.07090.9708-46.6616-37.6189-6.1187
26.56770.6831.25464.9326-0.26213.5424-0.00940.73240.1367-0.82030.21830.3396-0.34590.2155-0.16440.78970.00230.00410.57380.10690.668-37.4661-42.3694-4.1682
33.56773.93311.10226.5259-1.79564.4761-0.2470.7512-0.0273-0.94180.4928-0.4616-0.45091.1310.02861.3073-0.26460.20541.1304-0.20741.0632-21.8124-46.3477-11.3152
45.18096.2854-0.72217.904-0.86070.101-0.14730.8906-0.2002-1.5270.2344-1.6237-0.42550.00930.01392.1481-0.40320.3841.6764-0.18121.4038-14.6732-38.4592-18.555
58.0415-0.3613-0.07965.124-0.66233.0174-0.03530.91951.0639-0.6530.2711-0.5003-1.17680.8442-0.19221.0764-0.3260.2471.0495-0.07010.965-18.6768-33.8392-6.2008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 96 )A1 - 96
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 204 )A97 - 204
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 237 )A205 - 237
4X-RAY DIFFRACTION4chain 'A' and (resid 238 through 259 )A238 - 259
5X-RAY DIFFRACTION5chain 'A' and (resid 260 through 352 )A260 - 352

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