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- PDB-8jlm: Crystal structure of the Green fluorescent protein SET203EF223DA2... -

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Basic information

Entry
Database: PDB / ID: 8jlm
TitleCrystal structure of the Green fluorescent protein SET203EF223DA227 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: 1.85 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 SET203EF223DA227 variant at pH 4.5
Authors: Shin, S.C.
History
DepositionJun 2, 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

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9541
Polymers26,9541
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.240, 46.194, 123.239
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: 26954.344 Da / Num. of mol.: 1
Mutation: F64L,Q80R,S147D,N149Q,V163A,S175G,S202F,Q204E,A206T,F223D
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.: 138 / 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: 1.95 Å3/Da / Density % sol: 37.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M acetate pH 4.5, 25% (w/v) PEG 1500, 30% (w/v) MPD

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 17624 / % possible obs: 98.5 % / Redundancy: 7.4 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.035 / Rrim(I) all: 0.108 / Χ2: 1.29 / Net I/σ(I): 7.5 / Num. measured all: 129915
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.85-1.9240.35616790.4510.7880.1880.4050.70396.3
1.92-1.994.80.33417030.6410.8840.160.3730.80297.6
1.99-2.085.50.31517200.8050.9440.1390.3470.95898.1
2.08-2.1960.29617570.8550.960.1240.3231.07398.8
2.19-2.336.70.26217260.9120.9770.1030.2821.16998.8
2.33-2.517.20.22217510.9510.9870.0850.2391.28898.8
2.51-2.7680.18817630.9730.9930.0670.21.35999.5
2.76-3.169.10.12617850.9920.9980.0420.1331.45499.5
3.16-3.9910.60.07518090.9980.9990.0230.0791.52599.1
3.99-5011.10.05719310.99910.0170.061.52798.7

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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: 1.85→30.81 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 21.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 1760 10 %
Rwork0.193 --
obs0.1979 17592 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→30.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 0 138 1945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081844
X-RAY DIFFRACTIONf_angle_d1.0492493
X-RAY DIFFRACTIONf_dihedral_angle_d6.634242
X-RAY DIFFRACTIONf_chiral_restr0.065266
X-RAY DIFFRACTIONf_plane_restr0.01327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.35841210.29931096X-RAY DIFFRACTION91
1.9-1.960.30781340.27891196X-RAY DIFFRACTION97
1.96-2.020.28231300.25261178X-RAY DIFFRACTION98
2.02-2.090.25711340.22711204X-RAY DIFFRACTION98
2.09-2.170.27431330.21921190X-RAY DIFFRACTION99
2.17-2.270.27551340.20391203X-RAY DIFFRACTION99
2.27-2.390.27361360.20221223X-RAY DIFFRACTION99
2.39-2.540.22221340.18281221X-RAY DIFFRACTION99
2.54-2.740.23761380.18661230X-RAY DIFFRACTION99
2.74-3.010.24541360.18331230X-RAY DIFFRACTION99
3.02-3.450.2281380.16671242X-RAY DIFFRACTION99
3.45-4.340.17471410.15481264X-RAY DIFFRACTION99
4.35-30.810.23641510.18091355X-RAY DIFFRACTION100

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