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- PDB-6jc5: Crystal structure of the blue fluorescent protein with a Leu-Leu-... -

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Basic information

Entry
Database: PDB / ID: 6jc5
TitleCrystal structure of the blue fluorescent protein with a Leu-Leu-Gly tri-peptide chromophore derived from the purple chromoprotein of Stichodactyla haddoni
ComponentsshBFP
KeywordsFLUORESCENT PROTEIN / Sea anemone / Green fluorescent protein / UV absorption / emission spectra / biomarker
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / shBFP
Function and homology information
Biological speciesStichodactyla haddoni (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 Å
AuthorsKo, T.P. / Huang, K.F. / Chang, H.Y.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)104-2311-B-110-002-MY2 Taiwan
Academia Sinica (Taiwan)AS-KPQ-105-TPP Taiwan
Academia Sinica (Taiwan)107-0210-01-19-04 Taiwan
CitationJournal: Int. J. Biol. Macromol. / Year: 2019
Title: Crystal structure of the blue fluorescent protein with a Leu-Leu-Gly tri-peptide chromophore derived from the purple chromoprotein of Stichodactyla haddoni.
Authors: Chang, H.Y. / Ko, T.P. / Chang, Y.C. / Huang, K.F. / Lin, C.Y. / Chou, H.Y. / Chiang, C.Y. / Tsai, H.J.
History
DepositionJan 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: shBFP
B: shBFP
C: shBFP
D: shBFP
E: shBFP
F: shBFP
G: shBFP
H: shBFP


Theoretical massNumber of molelcules
Total (without water)208,6718
Polymers208,6718
Non-polymers00
Water21,0961171
1
A: shBFP
C: shBFP


Theoretical massNumber of molelcules
Total (without water)52,1682
Polymers52,1682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-13 kcal/mol
Surface area17930 Å2
MethodPISA
2
B: shBFP
D: shBFP


Theoretical massNumber of molelcules
Total (without water)52,1682
Polymers52,1682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-13 kcal/mol
Surface area17700 Å2
MethodPISA
3
E: shBFP
G: shBFP


Theoretical massNumber of molelcules
Total (without water)52,1682
Polymers52,1682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-14 kcal/mol
Surface area17860 Å2
MethodPISA
4
F: shBFP
H: shBFP


Theoretical massNumber of molelcules
Total (without water)52,1682
Polymers52,1682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-12 kcal/mol
Surface area17820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.567, 98.708, 197.493
Angle α, β, γ (deg.)90.00, 100.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-535-

HOH

21D-342-

HOH

31D-502-

HOH

41F-407-

HOH

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Components

#1: Protein
shBFP


Mass: 26083.873 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stichodactyla haddoni (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V8H022*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1171 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1M calcium acetate, 50% PEG 3350

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Data collection

DiffractionMean temperature: 123 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 163562 / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.8
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.668 / Num. unique obs: 12147

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JC6

6jc6


Resolution: 2.051→28.205 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9
RfactorNum. reflection% reflection
Rfree0.2078 2777 1.7 %
Rwork0.1722 --
obs0.1729 163562 90.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.051→28.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14076 0 0 1171 15247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414603
X-RAY DIFFRACTIONf_angle_d0.7819716
X-RAY DIFFRACTIONf_dihedral_angle_d14.9218680
X-RAY DIFFRACTIONf_chiral_restr0.0512060
X-RAY DIFFRACTIONf_plane_restr0.0042544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0509-2.08620.3136690.2513956X-RAY DIFFRACTION34
2.0862-2.12410.2564810.24894606X-RAY DIFFRACTION39
2.1241-2.1650.2507860.24674906X-RAY DIFFRACTION41
2.165-2.20920.3298880.24575078X-RAY DIFFRACTION43
2.2092-2.25720.2766960.24155453X-RAY DIFFRACTION46
2.2572-2.30960.25311040.23355887X-RAY DIFFRACTION49
2.3096-2.36740.24611060.22996046X-RAY DIFFRACTION51
2.3674-2.43140.22611070.23046170X-RAY DIFFRACTION52
2.4314-2.50290.28091110.22546449X-RAY DIFFRACTION55
2.5029-2.58360.23041250.22036894X-RAY DIFFRACTION58
2.5836-2.67590.27271350.20117530X-RAY DIFFRACTION64
2.6759-2.78290.22291360.18968336X-RAY DIFFRACTION70
2.7829-2.90940.251550.19529352X-RAY DIFFRACTION79
2.9094-3.06270.25151700.198510155X-RAY DIFFRACTION86
3.0627-3.25430.21431860.185111011X-RAY DIFFRACTION92
3.2543-3.50510.21112010.164911542X-RAY DIFFRACTION98
3.5051-3.85710.19462010.150111834X-RAY DIFFRACTION100
3.8571-4.41340.17042110.134411896X-RAY DIFFRACTION100
4.4134-5.55340.14752070.121811852X-RAY DIFFRACTION100
5.5534-28.20740.19592020.167811832X-RAY DIFFRACTION100

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