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- PDB-5b61: Extra-superfolder GFP -

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Basic information

Entry
Database: PDB / ID: 5b61
TitleExtra-superfolder GFP
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP / Random mutagenesis / Folding robustness
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.115 Å
AuthorsPark, H.H. / Jang, T.-H. / Choi, J.Y.
CitationJournal: FEBS Lett. / Year: 2017
Title: The mechanism of folding robustness revealed by the crystal structure of extra-superfolder GFP.
Authors: Choi, J.Y. / Jang, T.-H. / Park, H.H.
History
DepositionMay 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
C: Green fluorescent protein
D: Green fluorescent protein
E: Green fluorescent protein
F: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)160,8566
Polymers160,8566
Non-polymers00
Water0
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,8091
Polymers26,8091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,8091
Polymers26,8091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,8091
Polymers26,8091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,8091
Polymers26,8091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,8091
Polymers26,8091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,8091
Polymers26,8091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.301, 98.763, 263.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Green fluorescent protein /


Mass: 26809.328 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli (E. coli) / References: UniProt: P42212*PLUS

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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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% Polyethylene glycol 4000, 0.1M tris pH 8.5, 0.2M Lithium sulfate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 27784 / % possible obs: 97.8 % / Redundancy: 5.4 % / Net I/σ(I): 16.8

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.115→49.382 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 1401 5.04 %
Rwork0.1855 --
obs0.1893 27784 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.115→49.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10663 0 0 0 10663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110891
X-RAY DIFFRACTIONf_angle_d1.414711
X-RAY DIFFRACTIONf_dihedral_angle_d14.8574035
X-RAY DIFFRACTIONf_chiral_restr0.0591599
X-RAY DIFFRACTIONf_plane_restr0.0071934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1145-3.22580.33141390.24422391X-RAY DIFFRACTION91
3.2258-3.35490.28011270.22952647X-RAY DIFFRACTION98
3.3549-3.50760.29711190.2172664X-RAY DIFFRACTION98
3.5076-3.69250.26081360.20242641X-RAY DIFFRACTION99
3.6925-3.92370.3291490.19382633X-RAY DIFFRACTION98
3.9237-4.22650.23741420.17192633X-RAY DIFFRACTION98
4.2265-4.65160.2521520.14272637X-RAY DIFFRACTION98
4.6516-5.3240.19881370.13482681X-RAY DIFFRACTION98
5.324-6.7050.2221500.18552675X-RAY DIFFRACTION97
6.705-49.38770.24371500.19482781X-RAY DIFFRACTION96

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