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- PDB-8dhr: An ester mutant of SfGFP -

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Basic information

Entry
Database: PDB / ID: 8dhr
TitleAn ester mutant of SfGFP
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / beta barrel / ester mutant
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsReddi, R. / Valiyaveetil, F.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM087546 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: A facile approach for incorporating tyrosine esters to probe ion-binding sites and backbone hydrogen bonds.
Authors: Reddi, R. / Chatterjee, S. / Matulef, K. / Gustafson, A. / Gao, L. / Valiyaveetil, F.I.
History
DepositionJun 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)55,5462
Polymers55,5462
Non-polymers00
Water8,629479
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,7731
Polymers27,7731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,7731
Polymers27,7731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.917, 37.492, 91.848
Angle α, β, γ (deg.)90.000, 106.310, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-329-

HOH

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Components

#1: Protein Green fluorescent protein


Mass: 27773.193 Da / Num. of mol.: 2
Mutation: R30S, N39Y, L64F, R80Q, S99F, T105N, F145Y, T153M, A163V, V171I, V206A
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.93 Å3/Da / Density % sol: 36.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 mM Hepes, pH 7.5 and 25% Peg4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→45.15 Å / Num. obs: 42753 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.54 Å2 / CC1/2: 0.99 / Net I/σ(I): 15.5
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2475 / CC1/2: 0.84

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.75→44.08 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1883 1111 2.75 %
Rwork0.1806 39351 -
obs0.1808 40462 93.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.65 Å2 / Biso mean: 16.0848 Å2 / Biso min: 3.31 Å2
Refinement stepCycle: final / Resolution: 1.75→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 0 0 479 4053
Biso mean---26.42 -
Num. residues----452
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.830.23621240.23164461458585
1.83-1.930.22791340.20344604473888
1.93-2.050.20591330.18724857499092
2.05-2.20.21781420.1864960510295
2.2-2.430.19291400.18234980512095
2.43-2.780.21831450.19225099524497
2.78-3.50.16551450.17435152529797
3.5-44.080.15941480.16075238538696

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