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- PDB-4i3b: Crystal structure of fluorescent protein UnaG wild type -

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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


fatty acid transport / bioluminescence / fatty acid binding / nucleus / cytosol
Similarity search - Function
Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


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


Mass: 18.015 Da / Num. of mol.: 1923 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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