[English] 日本語
Yorodumi
- PDB-2pos: Crystal Structure of sylvaticin, a new secreted protein from pyth... -

+
Open data


ID or keywords:

Loading...

-
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 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


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


Mass: 18.015 Da / Num. of mol.: 734 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more