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- PDB-4i3d: Crystal structure of fluorescent protein UnaG N57A mutant -

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Basic information

Entry
Database: PDB / ID: 4i3d
TitleCrystal structure of fluorescent protein UnaG N57A 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: 2.298 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5828
Polymers62,2434
Non-polymers2,3394
Water11,458636
1
A: Bilirubin-inducible fluorescent protein UnaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1452
Polymers15,5611
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)16,1452
Polymers15,5611
Non-polymers5851
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)16,1452
Polymers15,5611
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)16,1452
Polymers15,5611
Non-polymers5851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.702, 73.702, 89.032
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 15560.746 Da / Num. of mol.: 4 / Mutation: N57A
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.: 4 / Source method: obtained synthetically / Formula: C33H36N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 636 / 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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate, 30%w/v Polyethylene glycol 8000, pH 6.5, 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: Jul 4, 2012
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.298→50 Å / Num. obs: 24074 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 29.17 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 15.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8

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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: 2.298→36.851 Å / Cross valid method: THROUGHOUT / σ(F): 2.08 / σ(I): 0 / Phase error: 19.01 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1616 1207 5.01 %RANDOM
Rwork0.1237 ---
all0.1272 24074 --
obs0.1272 24074 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.17 Å2
Refinement stepCycle: LAST / Resolution: 2.298→36.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 172 636 5184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084640
X-RAY DIFFRACTIONf_angle_d1.2566272
X-RAY DIFFRACTIONf_dihedral_angle_d17.8421780
X-RAY DIFFRACTIONf_chiral_restr0.069672
X-RAY DIFFRACTIONf_plane_restr0.005784
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2976-2.38930.23111230.1718251795
2.3893-2.49780.26711290.1696256895
2.4978-2.62910.21311170.144256496
2.6291-2.79310.20751550.1414248394
2.7931-3.00780.17791480.14253394
3.0078-3.30860.15231280.1227257695
3.3086-3.7830.15131360.1083250695
3.783-4.750.12011380.0956254095
4.75-17.36320.13641330.1228253695

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