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- PDB-4i3c: Crystal structure of fluorescent protein UnaG N57Q mutant -

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Basic information

Entry
Database: PDB / ID: 4i3c
TitleCrystal structure of fluorescent protein UnaG N57Q mutant
ComponentsBilirubin-inducible fluorescent protein UnaG
KeywordsFLUORESCENT PROTEIN / Bilirubin binding protein / Lipocalin / Beta barrel / Cytosol
Function / homology
Function and homology information


bioluminescence / lipid binding / cytoplasm
Similarity search - Function
Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-BLR / Bilirubin-inducible fluorescent protein UnaG
Similarity search - Component
Biological speciesAnguilla japonica (Japanese eel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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_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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Bilirubin-inducible fluorescent protein UnaG
B: Bilirubin-inducible fluorescent protein UnaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4054
Polymers31,2362
Non-polymers1,1692
Water15,421856
1
A: Bilirubin-inducible fluorescent protein UnaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2022
Polymers15,6181
Non-polymers5851
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)16,2022
Polymers15,6181
Non-polymers5851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.609, 70.609, 42.272
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 15617.797 Da / Num. of mol.: 2 / Mutation: N57Q
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.: 2 / Source method: obtained synthetically / Formula: C33H36N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 856 / 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: 1.95 Å3/Da / Density % sol: 36.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 30%w/v Polyethylene glycol monomethyl ether 2000, pH 8.0, 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: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2012
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 15849 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 12.46 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.8 / % possible all: 97.1

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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: 4I3B

4i3b


Resolution: 2.001→35.304 Å / Cross valid method: THROUGHOUT / σ(F): 1.97 / σ(I): 0 / Phase error: 17.57 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1776 799 5.26 %RANDOM
Rwork0.1473 ---
all0.1537 15197 --
obs0.1537 15197 95.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.46 Å2
Refinement stepCycle: LAST / Resolution: 2.001→35.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 86 856 3138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052328
X-RAY DIFFRACTIONf_angle_d1.1133146
X-RAY DIFFRACTIONf_dihedral_angle_d20.663896
X-RAY DIFFRACTIONf_chiral_restr0.057336
X-RAY DIFFRACTIONf_plane_restr0.003394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0015-2.12680.22291170.1762231588
2.1268-2.29080.23621160.1943209779
2.2908-2.52090.19051340.1558248994
2.5209-2.88480.1921420.1435249194
2.8848-3.6310.14761430.1264248994
3.631-19.97730.17121370.1475250694

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