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- PDB-3m3g: Crystal structure of Sm1, an elicitor of plant defence responses ... -

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Basic information

Entry
Database: PDB / ID: 3m3g
TitleCrystal structure of Sm1, an elicitor of plant defence responses from Trichoderma virens.
ComponentsEpl1 protein
KeywordsPOLYSACCHARIDE-BINDING PROTEIN / fungal / plant defense / fungus
Function / homology
Function and homology information


extracellular region / metal ion binding
Similarity search - Function
Cerato-platanin / Cerato-platanin / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / Epl1 protein
Similarity search - Component
Biological speciesHypocrea virens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.39 Å
AuthorsKrieger, I.V. / Vargas, W.A. / Kenerley, C.M. / Sacchettini, J.C.
CitationJournal: To be Published
Title: Crystal structure of Sm1, an elicitor of plant defence responses from Trichoderma virens.
Authors: Krieger, I.V. / Vargas, W.A. / Kenerley, C.M. / Sacchettini, J.C.
History
DepositionMar 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epl1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,58717
Polymers12,5551
Non-polymers1,03216
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.238, 46.365, 88.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Epl1 protein / Extracellular small protein 1


Mass: 12554.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: secreted / Source: (natural) Hypocrea virens (fungus) / Strain: Gv29-8 / References: UniProt: Q0R411
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 15mM ZnSO4, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91959 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2008
Details: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91959 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. all: 48167 / Num. obs: 40767 / Observed criterion σ(I): 3 / Redundancy: 6 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.142 / Net I/σ(I): 99.6
Reflection shellResolution: 1.39→1.41 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 9.4 / Num. unique all: 956 / Rsym value: 0.952

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.39→41.03 Å / SU ML: 0.17 / Isotropic thermal model: isotropic / σ(F): 0.42 / σ(I): 3 / Phase error: 18.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 3674 8.45 %random
Rwork0.1916 ---
obs0.193 40767 96.65 %-
all-48167 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.486 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 12.733 Å2
Refinement stepCycle: LAST / Resolution: 1.39→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms881 0 55 79 1015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006955
X-RAY DIFFRACTIONf_angle_d1.0651276
X-RAY DIFFRACTIONf_dihedral_angle_d14.916319
X-RAY DIFFRACTIONf_chiral_restr0.074137
X-RAY DIFFRACTIONf_plane_restr0.005165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3901-1.43980.312740.31563025X-RAY DIFFRACTION73
1.4398-1.49750.29733600.28093897X-RAY DIFFRACTION94
1.4975-1.56560.26283780.23674117X-RAY DIFFRACTION99
1.5656-1.64820.243720.2154091X-RAY DIFFRACTION100
1.6482-1.75140.21383820.18574123X-RAY DIFFRACTION100
1.7514-1.88670.18073870.16334109X-RAY DIFFRACTION100
1.8867-2.07650.16543850.15124091X-RAY DIFFRACTION100
2.0765-2.3770.18613750.15684141X-RAY DIFFRACTION100
2.377-2.99460.18493800.16854096X-RAY DIFFRACTION100
2.9946-41.04820.20723810.19714120X-RAY DIFFRACTION100

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