[English] 日本語
Yorodumi
- PDB-4i3b: Crystal structure of fluorescent protein UnaG wild type -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i3b
TitleCrystal structure of fluorescent protein UnaG wild type
ComponentsBilirubin-inducible fluorescent protein UnaG
KeywordsFLUORESCENT PROTEIN / Bilirubin binding protein / Lipocalin / Beta barrel / Fatty acid binding protein-like / Cytosol
Function / homology
Function and homology information


bioluminescence / lipid binding / cytoplasm
Similarity search - Function
Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-BLR / DI(HYDROXYETHYL)ETHER / Bilirubin-inducible fluorescent protein UnaG
Similarity search - Component
Biological speciesAnguilla japonica (Japanese eel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.199 Å
AuthorsKumagai, A. / Ando, R. / Miyatake, H. / Miyawaki, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: A bilirubin-inducible fluorescent protein from eel muscle
Authors: Kumagai, A. / Ando, R. / Miyatake, H. / Greimel, P. / Kobayashi, T. / Hirabayashi, Y. / Shimogori, T. / Miyawaki, A.
History
DepositionNov 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Feb 4, 2015Group: Database references / Non-polymer description
Revision 1.3Nov 8, 2023Group: 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bilirubin-inducible fluorescent protein UnaG
B: Bilirubin-inducible fluorescent protein UnaG
C: Bilirubin-inducible fluorescent protein UnaG
D: Bilirubin-inducible fluorescent protein UnaG
E: Bilirubin-inducible fluorescent protein UnaG
F: Bilirubin-inducible fluorescent protein UnaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,08621
Polymers93,6236
Non-polymers4,46315
Water34,6431923
1
A: Bilirubin-inducible fluorescent protein UnaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2953
Polymers15,6041
Non-polymers6912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bilirubin-inducible fluorescent protein UnaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5075
Polymers15,6041
Non-polymers9034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bilirubin-inducible fluorescent protein UnaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1882
Polymers15,6041
Non-polymers5851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Bilirubin-inducible fluorescent protein UnaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2953
Polymers15,6041
Non-polymers6912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Bilirubin-inducible fluorescent protein UnaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2953
Polymers15,6041
Non-polymers6912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Bilirubin-inducible fluorescent protein UnaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5075
Polymers15,6041
Non-polymers9034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.394, 73.954, 124.364
Angle α, β, γ (deg.)90.00, 92.45, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Bilirubin-inducible fluorescent protein UnaG / Unagi green fluorescent protein / UnaG


Mass: 15603.771 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anguilla japonica (Japanese eel) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0DM59
#2: Chemical
ChemComp-BLR / 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid / Bilirubin IX alpha / Bilirubin


Mass: 584.662 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H36N4O6
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1923 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, 20%w/v Polyethylene glycol 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2011
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.98→50 Å / Num. obs: 457015 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 10.01 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 35
Reflection shellResolution: 0.98→1 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 1.6 / % possible all: 27.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FDQ

1fdq


Resolution: 1.199→31.923 Å / SU ML: 0.1 / σ(F): 1.53 / Phase error: 14.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1586 11582 5 %
Rwork0.129 --
obs0.1305 231540 92.31 %
all-327679 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.01 Å2
Refinement stepCycle: LAST / Resolution: 1.199→31.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6539 0 321 1923 8783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127927
X-RAY DIFFRACTIONf_angle_d1.6710828
X-RAY DIFFRACTIONf_dihedral_angle_d17.0163253
X-RAY DIFFRACTIONf_chiral_restr0.0851141
X-RAY DIFFRACTIONf_plane_restr0.0091394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1989-1.21250.24222260.21574664X-RAY DIFFRACTION59
1.2125-1.22680.24252740.20455522X-RAY DIFFRACTION69
1.2268-1.24180.25053210.19585897X-RAY DIFFRACTION75
1.2418-1.25750.22553420.1976388X-RAY DIFFRACTION80
1.2575-1.2740.22983830.18466910X-RAY DIFFRACTION88
1.274-1.29150.2213530.16757111X-RAY DIFFRACTION90
1.2915-1.30990.20844060.16087123X-RAY DIFFRACTION90
1.3099-1.32950.20463690.15147187X-RAY DIFFRACTION91
1.3295-1.35030.17963980.14467241X-RAY DIFFRACTION91
1.3503-1.37240.18983720.13477234X-RAY DIFFRACTION92
1.3724-1.39610.19443810.13167308X-RAY DIFFRACTION92
1.3961-1.42150.17953920.12797389X-RAY DIFFRACTION93
1.4215-1.44880.19363960.12267415X-RAY DIFFRACTION94
1.4488-1.47840.16253750.11267516X-RAY DIFFRACTION94
1.4784-1.51050.1574030.10717457X-RAY DIFFRACTION95
1.5105-1.54570.15563950.10967623X-RAY DIFFRACTION96
1.5457-1.58430.1584170.10797626X-RAY DIFFRACTION96
1.5843-1.62710.15953750.10457696X-RAY DIFFRACTION96
1.6271-1.6750.14963900.10077702X-RAY DIFFRACTION97
1.675-1.72910.1393920.10797774X-RAY DIFFRACTION98
1.7291-1.79090.15524490.11597787X-RAY DIFFRACTION98
1.7909-1.86260.15054290.11417850X-RAY DIFFRACTION99
1.8626-1.94730.154030.11477911X-RAY DIFFRACTION99
1.9473-2.050.13983760.11347956X-RAY DIFFRACTION100
2.05-2.17840.13774000.10937965X-RAY DIFFRACTION100
2.1784-2.34650.13234030.11757991X-RAY DIFFRACTION100
2.3465-2.58260.15334400.13317935X-RAY DIFFRACTION100
2.5826-2.95610.16424290.13648012X-RAY DIFFRACTION100
2.9561-3.72340.13734770.12287912X-RAY DIFFRACTION99
3.7234-31.93420.1644160.15317856X-RAY DIFFRACTION97

+
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