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- PDB-8jkc: Crystal structure of the Green fluorescent protein SE_A277 varian... -

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Basic information

Entry
Database: PDB / ID: 8jkc
TitleCrystal structure of the Green fluorescent protein SE_A277 variant at pH 4.5
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / bioimaging / Sensor. GFP
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 / Resolution: 1.95 Å
AuthorsShin, S.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of the Green fluorescent protein SE_A277 variant at pH 4.5
Authors: Shin, S.C.
History
DepositionJun 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 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
C: Green fluorescent protein
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)107,8344
Polymers107,8344
Non-polymers00
Water10,233568
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9581
Polymers26,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9581
Polymers26,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9581
Polymers26,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9581
Polymers26,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.787, 80.632, 179.331
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: 26958.420 Da / Num. of mol.: 4
Mutation: F64L,Q80R,S147D,N149Q,V163A,S175G,S202F,Q204T,A206T
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.: 568 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1M sodium acetate pH 4.5, 2.2M Sodium Chloride

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 80378 / % possible obs: 99.2 % / Redundancy: 8.3 % / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.041 / Rrim(I) all: 0.133 / Χ2: 1.473 / Net I/σ(I): 5.2 / Num. measured all: 664241
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.95-2.024.50.41576890.280.6610.2020.4640.46896.3
2.02-2.15.50.40779080.4170.7670.1790.4480.5398.8
2.1-2.26.30.37979390.670.8960.1550.4110.60199.3
2.2-2.316.90.35679860.7860.9380.1380.3830.67599.4
2.31-2.467.50.30180180.9160.9780.110.3210.79599.6
2.46-2.658.20.25579840.9570.9890.0890.270.90499.6
2.65-2.9190.20480970.9750.9940.0680.2151.06699.6
2.91-3.3310.30.13680720.9890.9970.0420.1421.43499.7
3.33-4.211.70.09681990.9940.9980.0280.12.04799.8
4.2-5012.20.08484860.990.9980.0240.0883.39399.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48.02 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 2002 2.49 %
Rwork0.2011 --
obs0.2022 80308 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7228 0 0 568 7796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087396
X-RAY DIFFRACTIONf_angle_d1.1219996
X-RAY DIFFRACTIONf_dihedral_angle_d6.822968
X-RAY DIFFRACTIONf_chiral_restr0.0631068
X-RAY DIFFRACTIONf_plane_restr0.0081304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.36661360.31244912X-RAY DIFFRACTION88
1.99-2.050.33141360.29675521X-RAY DIFFRACTION98
2.05-2.110.30991300.27475533X-RAY DIFFRACTION99
2.11-2.180.3531480.26055594X-RAY DIFFRACTION99
2.18-2.250.27971480.24265553X-RAY DIFFRACTION99
2.25-2.340.26441430.23095563X-RAY DIFFRACTION99
2.34-2.450.26711440.20825635X-RAY DIFFRACTION100
2.45-2.580.22811400.19695604X-RAY DIFFRACTION100
2.58-2.740.25241410.20055627X-RAY DIFFRACTION100
2.74-2.950.25061450.19995638X-RAY DIFFRACTION100
2.95-3.250.25431420.1865689X-RAY DIFFRACTION100
3.25-3.720.19881460.17775690X-RAY DIFFRACTION100
3.72-4.690.19341430.15185777X-RAY DIFFRACTION100
4.69-48.020.23221600.18545970X-RAY DIFFRACTION100

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