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- PDB-2pr0: Crystal structure of Sylvaticin, a new secreted protein from Pyth... -

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Basic information

Entry
Database: PDB / ID: 2pr0
TitleCrystal structure of Sylvaticin, a new secreted protein from Pythium Sylvaticum
Componentssylvaticin
KeywordsTOXIN / elicitin
Function / homology
Function and homology information


symbiont-mediated perturbation of host programmed cell death / extracellular region
Similarity search - Function
Beta-cryptogein / Elicitin domain / Elicitin / Elicitin superfamily / Elicitin / Elicitin / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Elicitin
Similarity search - Component
Biological speciesPythium sylvaticum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsLascombe, M.B. / Prange, T. / Retailleau, P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of sylvaticin, a new alpha-elicitin-like protein from Pythium sylvaticum.
Authors: Lascombe, M.B. / Retailleau, P. / Ponchet, M. / Industri, B. / Blein, J.P. / Prange, T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Purification, crystallization and preliminary X-ray studies of sylvaticin, an elicitin-like protein from Pythium sylvaticum
Authors: Lascombe, M.-B. / Ponchet, M. / Cardin, L. / Milat, M.-L. / Blein, J.-P. / Prange, T.
History
DepositionMay 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence The sequence of this protein is not available in the UNP database at the time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: sylvaticin
B: sylvaticin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1846
Polymers20,8222
Non-polymers3624
Water3,765209
1
A: sylvaticin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5923
Polymers10,4111
Non-polymers1812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: sylvaticin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5923
Polymers10,4111
Non-polymers1812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.692, 25.974, 68.349
Angle α, β, γ (deg.)90.000, 99.690, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein sylvaticin


Mass: 10411.029 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pythium sylvaticum (eukaryote) / Strain: strain 37 / References: UniProt: D0VWX7*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 2000 MME, 0.01M NiCl2, 0.1M Tris-HKL pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.480, 1.239
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 14, 2003 / Details: mirrors
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.481
21.2391
ReflectionResolution: 1.72→26 Å / Num. obs: 18321 / % possible obs: 92.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.2
Reflection shellResolution: 1.72→1.82 Å / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 12.5 / % possible all: 71.8

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.72→25.9 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1857 1757 -RANDOM
Rwork0.1939 ---
all0.204 20145 --
obs0.204 18321 99.4 %-
Displacement parametersBiso mean: 19.444 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati sigma a obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.72→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 0 18 209 1683
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d3.19
X-RAY DIFFRACTIONc_dihedral_angle_d25.56
X-RAY DIFFRACTIONc_improper_angle_d3.71
LS refinement shellResolution: 1.72→1.78 Å
RfactorNum. reflection% reflection
Rfree0.254 100 -
Rwork0.2639 --
obs-968 52 %

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