[English] 日本語
Yorodumi
- PDB-3f2e: Crystal structure of Yellowstone SIRV coat protein C-terminus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f2e
TitleCrystal structure of Yellowstone SIRV coat protein C-terminus
ComponentsSIRV coat protein
KeywordsVIRAL PROTEIN / four helix bundle / virus coat protein
Function / homologySulfolobus virus, coat protein, C-terminal / Sulfolobus virus coat protein C terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #800 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / CITRIC ACID / SIRV coat protein
Function and homology information
Biological speciesSulfolobus islandicus rudivirus 1 variant YNP
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.668 Å
AuthorsTaurog, R.E. / Szymczyna, B.R. / Williamson, J.R. / Johnson, J.E.
CitationJournal: Structure / Year: 2009
Title: Synergy of NMR, computation, and X-ray crystallography for structural biology.
Authors: Szymczyna, B.R. / Taurog, R.E. / Young, M.J. / Snyder, J.C. / Johnson, J.E. / Williamson, J.R.
History
DepositionOct 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value ..._reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SIRV coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6912
Polymers10,4991
Non-polymers1921
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.410, 54.410, 77.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein SIRV coat protein


Mass: 10498.848 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Details: pET31a tags were removed from the vector, a C-terminal hexahistidine tag was cloned in
Source: (gene. exp.) Sulfolobus islandicus rudivirus 1 variant YNP
Plasmid: pET31a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLySs / References: UniProt: D0VX05*PLUS
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop
Details: SIRV CP (residues 46-134) at 19 or 30 mg/ml in 20 mM Na MES pH 6.0 was mixed 1:1 with 25% PEG 20,000, 0.1 M Na Citrate pH 3.6, 4-9% sucrose. Crystals were frozen in of 14% PEG 20,000, 50 mM ...Details: SIRV CP (residues 46-134) at 19 or 30 mg/ml in 20 mM Na MES pH 6.0 was mixed 1:1 with 25% PEG 20,000, 0.1 M Na Citrate pH 3.6, 4-9% sucrose. Crystals were frozen in of 14% PEG 20,000, 50 mM sodium citrate pH 3.6, 15-25% sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 299K

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.668→44.588 Å / Num. obs: 14062 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 16.8 % / Biso Wilson estimate: 24.675 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.062 / Net I/σ(I): 33.4
Reflection shellResolution: 1.668→1.7 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 8.27 / Num. unique all: 965 / Rsym value: 0.371 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CS-Rosetta model

Resolution: 1.668→31.642 Å / SU ML: 0.14 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 703 5 %random
Rwork0.1837 ---
obs0.1846 14055 99.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.566 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.2583 Å2-0 Å2-0 Å2
2---0.2583 Å20 Å2
3----5.774 Å2
Refine analyzeLuzzati coordinate error obs: 0.177 Å
Refinement stepCycle: LAST / Resolution: 1.668→31.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms600 0 13 80 693
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_deg0.833
X-RAY DIFFRACTIONf_dihedral_angle_d15.532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.668-1.79710.23131340.1832541254197
1.7971-1.97790.19541380.17532623262399
1.9779-2.26410.17781400.163926572657100
2.2641-2.85220.17711420.179226912691100
2.8522-31.64740.21841490.18728402840100

+
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