[English] 日本語
Yorodumi
- PDB-5f6z: Sandercyanin Fluorescent Protein purified from Sander vitreus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f6z
TitleSandercyanin Fluorescent Protein purified from Sander vitreus
ComponentsSandercyanin Fluorescent Protein
KeywordsFLUORESCENT PROTEIN / Sandercyanin Fluorescent Protein (SFP) / walleye / lipocalin / photo-stability / red fluorescent protein
Function / homology
Function and homology information


Lipocalin-like domain / Invertebrate colouration protein / Lipocalin, ApoD type / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Sandercyanin Fluorescent Protein
Similarity search - Component
Biological speciesSander vitreus (walleye)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.248 Å
AuthorsGhosh, S. / Yu, C.L. / Ferraro, D. / Sudha, S. / Pal, S. / Schaefer, W. / Gibson, D.T. / Subramanian, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Blue protein with red fluorescence
Authors: Ghosh, S. / Yu, C.L. / Ferraro, D.J. / Sudha, S. / Pal, S.K. / Schaefer, W.F. / Gibson, D.T. / Ramaswamy, S.
History
DepositionDec 7, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,39912
Polymers74,1844
Non-polymers3,2158
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-112 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.394, 93.394, 246.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-383-

HOH

-
Components

#1: Protein
Sandercyanin Fluorescent Protein


Mass: 18545.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sander vitreus (walleye) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1D5B369*PLUS
#2: Chemical
ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.78 % / Description: Blue crystals rectangular in shape
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M sodium acetate, 3M magnesium sulphate hydrate, 20% PEG 8000

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0210.979
SYNCHROTRONAPS 17-ID21.0414, 1.0405, 1.033
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELAug 15, 2008
ADSC QUANTUM 2102CCDJul 8, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Au filterSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.04141
31.04051
41.0331
ReflectionResolution: 2.248→19.84 Å / Num. obs: 52052 / % possible obs: 98.63 % / Redundancy: 3.4 % / Net I/σ(I): 5.86
Reflection shellResolution: 2.248→2.329 Å

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
d*TREKdata reduction
d*TREKdata scaling
d*TREKphasing
RefinementMethod to determine structure: MAD / Resolution: 2.248→19.835 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3116 2000 3.84 %
Rwork0.2369 --
obs0.2398 52045 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.248→19.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5079 0 228 324 5631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095463
X-RAY DIFFRACTIONf_angle_d1.2887450
X-RAY DIFFRACTIONf_dihedral_angle_d16.2081988
X-RAY DIFFRACTIONf_chiral_restr0.072798
X-RAY DIFFRACTIONf_plane_restr0.007957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2483-2.30440.42481390.37223487X-RAY DIFFRACTION98
2.3044-2.36660.43211420.34983568X-RAY DIFFRACTION100
2.3666-2.43610.40241430.33163560X-RAY DIFFRACTION100
2.4361-2.51460.3461430.31263576X-RAY DIFFRACTION100
2.5146-2.60430.38081430.31073567X-RAY DIFFRACTION100
2.6043-2.70830.411420.29933573X-RAY DIFFRACTION100
2.7083-2.83130.36081440.27573606X-RAY DIFFRACTION100
2.8313-2.98010.32881430.25183571X-RAY DIFFRACTION100
2.9801-3.16610.32941440.23543592X-RAY DIFFRACTION100
3.1661-3.40940.28451440.20543616X-RAY DIFFRACTION100
3.4094-3.75040.26781450.18743630X-RAY DIFFRACTION99
3.7504-4.28830.24281460.16753639X-RAY DIFFRACTION99
4.2883-5.38490.24121450.16393650X-RAY DIFFRACTION98
5.3849-19.83550.26881370.21083410X-RAY DIFFRACTION87
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.17950.08260.230.3619-0.13920.4756-0.0964-0.14230.05550.1262-0.0029-0.05350.0442-0.1138-0.00430.15740.03530.00330.25190.01380.2006-2.710621.7368-10.1038
20.2410.0117-0.28770.0086-0.00670.3323-0.0060.0378-0.1161-0.0597-0.070.022-0.1290.052-00.1941-0.0174-0.03140.27580.02020.270512.818141.5588-42.0827
30.40680.4217-0.0480.5092-0.2480.5952-0.08770.14210.04210.0430.1315-0.0775-0.0638-0.06070.0020.1765-0.04540.01740.3356-0.00360.2229-16.467923.1214-42.635
40.3037-0.2072-0.49310.55330.25280.7463-0.03020.0375-0.04830.0236-0.07380.1685-0.278-0.023300.33480.0359-0.070.22120.00350.2518-9.025254.7485-18.1049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 20:185)
2X-RAY DIFFRACTION2chain 'B' and (resseq 20:185)
3X-RAY DIFFRACTION3chain 'C' and (resseq 20:185)
4X-RAY DIFFRACTION4chain 'D' and (resseq 20:185)

+
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