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- PDB-2pos: Crystal Structure of sylvaticin, a new secreted protein from pyth... -

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Basic information

Entry
Database: PDB / ID: 2pos
TitleCrystal Structure of sylvaticin, a new secreted protein from pythium sylvaticum
ComponentsSYLVATICIN
KeywordsTOXIN / sylvaticin / elicitin
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense-related 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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLascombe, M.B. / Prange, T.
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,crystallisation 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
DepositionApr 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: 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_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SYLVATICIN
B: SYLVATICIN
C: SYLVATICIN
D: SYLVATICIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,40313
Polymers41,6444
Non-polymers7599
Water13,223734
1
A: SYLVATICIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6274
Polymers10,4111
Non-polymers2163
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
3
C: SYLVATICIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5923
Polymers10,4111
Non-polymers1812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 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)36.220, 46.000, 55.730
Angle α, β, γ (deg.)85.20, 71.27, 74.63
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
SYLVATICIN


Mass: 10411.029 Da / Num. of mol.: 4 / 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 / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


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


Mass: 18.015 Da / Num. of mol.: 734 / 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: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 40% PEG 2000MME, 10mM NiCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2007
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.6→33 Å / Num. all: 43901 / Num. obs: 40560 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.041 / Net I/σ(I): 18.1
Reflection shellResolution: 1.59→1.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 9.22 / Num. unique all: 6468 / Rsym value: 0.1 / % possible all: 91.3

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å26.39 Å
Translation2.5 Å26.39 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Sylvaticin C2

Resolution: 1.6→21.06 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.63 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.1 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2024 5 %RANDOM
Rwork0.15 ---
all0.152 43341 --
obs0.152 40262 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.769 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→21.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 37 734 3701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223057
X-RAY DIFFRACTIONr_angle_refined_deg1.111.9934176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7675378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.40326.033121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80615494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.956154
X-RAY DIFFRACTIONr_chiral_restr0.070.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022296
X-RAY DIFFRACTIONr_nbd_refined0.2050.21580
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22181
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2578
X-RAY DIFFRACTIONr_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.2129
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.293
X-RAY DIFFRACTIONr_mcbond_it0.4971.51970
X-RAY DIFFRACTIONr_mcangle_it0.89723120
X-RAY DIFFRACTIONr_scbond_it1.6131223
X-RAY DIFFRACTIONr_scangle_it2.6474.51056
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 146 -
Rwork0.164 2875 -
obs-3021 93.67 %

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