[English] 日本語
Yorodumi
- PDB-3is2: 2.3 Angstrom Crystal Structure of a Cys71 Sulfenic Acid form of Vivid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3is2
Title2.3 Angstrom Crystal Structure of a Cys71 Sulfenic Acid form of Vivid
Components(Vivid PAS protein VVD) x 2
KeywordsSIGNALING PROTEIN / Photoreceptor / Circadian Clock / Flavin / Sulfenic Acid
Function / homology
Function and homology information


nucleotide binding / nucleus
Similarity search - Function
PAS domain / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Vivid PAS protein VVD
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZoltowski, B.D. / Lamb, J.S. / Pabit, S.A. / Li, L. / Pollack, L. / Crane, B.R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Illuminating solution responses of a LOV domain protein with photocoupled small-angle X-ray scattering.
Authors: Lamb, J.S. / Zoltowski, B.D. / Pabit, S.A. / Li, L. / Crane, B.R. / Pollack, L.
History
DepositionAug 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vivid PAS protein VVD
B: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6134
Polymers35,0422
Non-polymers1,5712
Water6,539363
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-31 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.420, 81.110, 58.030
Angle α, β, γ (deg.)90.00, 95.03, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe crystal structure contains a dimer in the asymmetric unit, however the physiologically relevant photo-induced dimer is currently unknown.

-
Components

#1: Protein Vivid PAS protein VVD


Mass: 17529.004 Da / Num. of mol.: 1 / Fragment: VVD-36 (UNP RESIDUES 37-186)
Source method: isolated from a genetically manipulated source
Details: CSO at position 71 / Source: (gene. exp.) Neurospora crassa (fungus) / Gene: G17A4.050, Vivid, vvd / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9C3Y6
#2: Protein Vivid PAS protein VVD


Mass: 17513.004 Da / Num. of mol.: 1 / Fragment: VVD-36 (UNP RESIDUES 37-186)
Source method: isolated from a genetically manipulated source
Details: CYS at position 71 / Source: (gene. exp.) Neurospora crassa (fungus) / Gene: G17A4.050, Vivid, vvd / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9C3Y6
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20 mM imidazole, 26% PEG 4000, 100 mM trisodium citrate, 100 mM NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F3 / Wavelength: 1.28 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 20, 2007
RadiationMonochromator: Double-bounce downward, offset 25 -110 mm / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 15003 / Num. obs: 14822 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 24.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1504 -Random
Rwork0.226 ---
all0.254 15003 --
obs0.254 14822 98.8 %-
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 106 363 2849

+
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