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- PDB-3h2j: Crystal structure of the rice cell wall degrading esterase LipA f... -

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Basic information

Entry
Database: PDB / ID: 3h2j
TitleCrystal structure of the rice cell wall degrading esterase LipA from Xanthomonas oryzae
Componentsesterase
KeywordsHYDROLASE / Xanthomonas oryzae pv. oryzae / esterase / cell wall degrading enzyme / rice / virulence / innate immune responses / pathogenesis / glycoside binding
Function / homology
Function and homology information


triacylglycerol lipase activity / aminopeptidase activity / lipid catabolic process
Similarity search - Function
Secretory lipase / Lipase, secreted / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dipeptidyl aminopeptidases/acylaminoacyl-peptidases
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsAparna, G. / Chatterjee, A. / Sonti, R.V. / Sankaranarayanan, R.
CitationJournal: Plant Cell / Year: 2009
Title: A Cell Wall-Degrading Esterase of Xanthomonas oryzae Requires a Unique Substrate Recognition Module for Pathogenesis on Rice
Authors: Aparna, G. / Chatterjee, A. / Sonti, R.V. / Sankaranarayanan, R.
History
DepositionApr 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: esterase


Theoretical massNumber of molelcules
Total (without water)42,6631
Polymers42,6631
Non-polymers00
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.130, 62.370, 66.150
Angle α, β, γ (deg.)90.00, 90.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein esterase / Putative uncharacterized protein


Mass: 42662.637 Da / Num. of mol.: 1 / Fragment: residues in UNP 45-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Strain: BXO43 / Gene: LipA / Plasmid: pHM1 / Production host: Xanthomonas oryzae pv. oryzae (bacteria) / Strain (production host): BXO43
References: UniProt: Q5H5J0, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 48% PEG 400, 0.10M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→25 Å / Num. obs: 27294 / Biso Wilson estimate: 19.9 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H2G

3h2g


Resolution: 1.89→24.2 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1612603.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1389 5.1 %RANDOM
Rwork0.193 ---
obs0.193 27294 90.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.0006 Å2 / ksol: 0.361392 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å2-6.39 Å2
2--3.23 Å20 Å2
3----0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.89→24.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 0 324 3258
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 1.89→1.96 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.301 121 5.6 %
Rwork0.263 2056 -
obs--72.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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