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- PDB-1y7h: Structural and biochemical studies identify tobacco SABP2 as a me... -

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Basic information

Entry
Database: PDB / ID: 1y7h
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 / Protein Structure Initiative / PSI / 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
THIOCYANATE ION / Salicylic acid-binding protein 2
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.52 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 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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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
C: salicylic acid-binding protein 2
D: salicylic acid-binding protein 2
E: salicylic acid-binding protein 2
F: salicylic acid-binding protein 2
G: salicylic acid-binding protein 2
H: salicylic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,11216
Polymers246,6488
Non-polymers4658
Water4,035224
1
A: salicylic acid-binding protein 2
B: salicylic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7784
Polymers61,6622
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-23 kcal/mol
Surface area20310 Å2
MethodPISA
2
C: salicylic acid-binding protein 2
D: salicylic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7784
Polymers61,6622
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-26 kcal/mol
Surface area20210 Å2
MethodPISA
3
E: salicylic acid-binding protein 2
F: salicylic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7784
Polymers61,6622
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-24 kcal/mol
Surface area19990 Å2
MethodPISA
4
G: salicylic acid-binding protein 2
H: salicylic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7784
Polymers61,6622
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-25 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.630, 137.736, 171.208
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30830.977 Da / Num. of mol.: 8
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-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M sodium thiocyanate, 5 mM spermine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 12, 2003 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→28.17 Å / Num. all: 1410442 / Num. obs: 138444 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.44 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 12.18
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.13 / Num. unique all: 13511 / Rsym value: 0.309 / % possible all: 97.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.52→28.17 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 277179.93 / 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
Rfree0.297 12883 9.9 %RANDOM
Rwork0.227 ---
all0.229 138444 --
obs0.227 130389 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.0335 Å2 / ksol: 0.307111 e/Å3
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-1.28 Å2
2---0.3 Å20 Å2
3---1.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.52→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16331 0 24 224 16579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 1624 10.2 %
Rwork0.248 14373 -
obs-14373 66.7 %

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