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- PDB-1y7i: Structural and biochemical studies identify tobacco SABP2 as a me... -

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Basic information

Entry
Database: PDB / ID: 1y7i
TitleStructural and biochemical studies identify tobacco SABP2 as a methylsalicylate esterase and further implicate it in plant innate immunity, Northeast Structural Genomics Target AR2241
Componentssalicylic acid-binding protein 2
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


jasmonic acid metabolic process / methyl salicylate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process / methyl indole-3-acetate esterase activity / systemic acquired resistance, salicylic acid mediated signaling pathway / lipase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / innate immune response
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / Lipases, serine active site. / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-HYDROXYBENZOIC ACID / Salicylic acid-binding protein 2
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsForouhar, F. / Yang, Y. / Kumar, D. / Chen, Y. / Fridman, E. / Park, S.W. / Chiang, Y. / Acton, T.B. / Montelione, G.T. / Pichersky, E. ...Forouhar, F. / Yang, Y. / Kumar, D. / Chen, Y. / Fridman, E. / Park, S.W. / Chiang, Y. / Acton, T.B. / Montelione, G.T. / Pichersky, E. / Klessig, D.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structural and biochemical studies identify tobacco SABP2 as a methyl salicylate esterase and implicate it in plant innate immunity
Authors: Forouhar, F. / Yang, Y. / Kumar, D. / Chen, Y. / Fridman, E. / Park, S.W. / Chiang, Y. / Acton, T.B. / Montelione, G.T. / Pichersky, E. / Klessig, D.F. / Tong, L.
History
DepositionDec 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: salicylic acid-binding protein 2
B: salicylic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0765
Polymers61,6622
Non-polymers4143
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-10 kcal/mol
Surface area20050 Å2
MethodPISA
2
A: salicylic acid-binding protein 2
B: salicylic acid-binding protein 2
hetero molecules

A: salicylic acid-binding protein 2
B: salicylic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,15310
Polymers123,3244
Non-polymers8296
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7360 Å2
ΔGint-19 kcal/mol
Surface area38110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.221, 48.024, 92.590
Angle α, β, γ (deg.)90.00, 110.63, 90.00
Int Tables number5
Space group name H-MC121
DetailsMonomer. Although the two monomers in ASU form a dimer, the biochemical data suggest that SABP2 acts as a monomer.

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Components

#1: Protein salicylic acid-binding protein 2 / SABP2


Mass: 30830.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q6RYA0
#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 10 mM SA, 0.2 M calcium acetate, 10 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.1→29.53 Å / Num. all: 34843 / Num. obs: 34275 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.057 / Net I/σ(I): 15.51
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3.47 / Num. unique all: 3227 / Rsym value: 0.261 / % possible all: 94

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y7H
Resolution: 2.1→29.53 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 353462.51 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3152 10 %RANDOM
Rwork0.197 ---
all0.202 32275 --
obs0.197 31540 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.8219 Å2 / ksol: 0.327334 e/Å3
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.54 Å20 Å25.9 Å2
2--0.38 Å20 Å2
3---3.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4121 0 30 461 4612
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 458 10.7 %
Rwork0.217 3842 -
obs-3842 76.5 %

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