[English] 日本語
Yorodumi
- PDB-7vnl: Sandercyanin mutant-F55A-Biliverdin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vnl
TitleSandercyanin mutant-F55A-Biliverdin complex
ComponentsSandercyanin Fluorescent Protein
KeywordsFLUORESCENT PROTEIN / Lipocalin / biliverdin
Function / homology
Function and homology information


pigment binding / response to reactive oxygen species / lipid metabolic process / lipid binding / extracellular region / cytoplasm
Similarity search - Function
Lipocalin-like domain / Invertebrate colouration protein / Lipocalin, ApoD type / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Apolipoprotein D
Similarity search - Component
Biological speciesSander vitreus (walleye)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsYadav, K. / Ghosh, S. / Subramanian, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5801/INF/22/156/2012 India
CitationJournal: Febs Lett. / Year: 2022
Title: Phenylalanine stacking enhances the red fluorescence of biliverdin IX alpha on UV excitation in sandercyanin fluorescent protein.
Authors: Yadav, K. / Ghosh, S. / Barak, A. / Schaefer, W. / Subramanian, R.
History
DepositionOct 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sandercyanin Fluorescent Protein
B: Sandercyanin Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7216
Polymers40,1672
Non-polymers1,5544
Water3,765209
1
A: Sandercyanin Fluorescent Protein
B: Sandercyanin Fluorescent Protein
hetero molecules

A: Sandercyanin Fluorescent Protein
B: Sandercyanin Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,44212
Polymers80,3354
Non-polymers3,1078
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Buried area14350 Å2
ΔGint-127 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.388, 158.388, 81.073
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

-
Components

#1: Protein Sandercyanin Fluorescent Protein


Mass: 20083.652 Da / Num. of mol.: 2 / Mutation: F55A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sander vitreus (walleye) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D5B367
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.5 % / Description: Rod shaped and hexagonal
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M sodium malonate pH 7, 12% PEG w/v 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9897 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9897 Å / Relative weight: 1
ReflectionResolution: 1.93→79.12 Å / Num. obs: 45351 / % possible obs: 100 % / Redundancy: 74.4 % / Biso Wilson estimate: 35.59 Å2 / CC1/2: 1 / Rpim(I) all: 0.026 / Rrim(I) all: 0.229 / Net I/σ(I): 20.8
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 74.8 % / Num. unique obs: 6479 / CC1/2: 0.586 / Rpim(I) all: 0.581 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALA3.3.22data scaling
PHENIX1.15.2-3472phasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EZ2

5ez2


Resolution: 1.93→52.36 Å / SU ML: 0.2237 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.1849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.225 2263 5.01 %
Rwork0.1933 42938 -
obs0.1949 45201 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.28 Å2
Refinement stepCycle: LAST / Resolution: 1.93→52.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 112 209 2909
Refine LS restraintsType: f_bond_d / Dev ideal: 0.0078 / Number: 2768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.3241430.32462589X-RAY DIFFRACTION98.88
1.97-2.020.31531410.29692617X-RAY DIFFRACTION99.21
2.02-2.070.37171200.272656X-RAY DIFFRACTION99.36
2.07-2.120.26611470.22872627X-RAY DIFFRACTION99.57

+
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