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- PDB-1yhg: Uncyclized precursor structure of S65G Y66S V68G GFP variant -

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Basic information

Entry
Database: PDB / ID: 1yhg
TitleUncyclized precursor structure of S65G Y66S V68G GFP variant
Componentsgreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / chromophore uncyclized dimer
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: 2.5 Å
AuthorsBarondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D.
Citation
Journal: Biochemistry / Year: 2005
Title: Understanding GFP Chromophore Biosynthesis: Controlling Backbone Cyclization and Modifying Post-translational Chemistry.
Authors: Barondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures
Authors: Barondeau, D.P. / Putnam, C.D. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D.
History
DepositionJan 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)53,3862
Polymers53,3862
Non-polymers00
Water2,324129
1
A: green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,6931
Polymers26,6931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,6931
Polymers26,6931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.301, 71.098, 60.940
Angle α, β, γ (deg.)90, 94.765, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein green fluorescent protein


Mass: 26692.943 Da / Num. of mol.: 2 / Mutation: F64L, S65G, Y66S, V68G, F99S, M153T, V163A
Source method: isolated from a genetically manipulated source
Details: F64L, S65G, Y66S, V68G, F99S, M153T, V163A / Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.83 Å3/Da / Density % sol: 32.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, 50 mM MgCl2, 50 mM Hepes 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97975 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97975 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 13380 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.119 / Χ2: 1.528 / Net I/σ(I): 17.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.312 / Num. unique all: 1324 / Χ2: 1.342 / % possible all: 99.7

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Processing

Software
NameClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 671 5 %Random
Rwork0.213 ---
all0.213 13145 --
obs0.213 12474 97.9 %-
Displacement parametersBiso mean: 10 Å2
Baniso -1Baniso -2Baniso -3
1-3.036 Å20 Å21.623 Å2
2---2.587 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 0 129 3666
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6

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