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- PDB-5z6y: Structure of sfYFP48S95C66BPA -

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Basic information

Entry
Database: PDB / ID: 5z6y
TitleStructure of sfYFP48S95C66BPA
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / chromophore linkage electron transfer
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 / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.87 Å
AuthorsWang, J.Y. / Wang, J.Y.
CitationJournal: To Be Published
Title: structure of sfYFP48S95C66BPA at 1.95 Angstroms resolution
Authors: Wang, J.Y. / Wang, J.Y.
History
DepositionJan 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: 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)25,8971
Polymers25,8971
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10410 Å2
Unit cell
Length a, b, c (Å)51.574, 51.574, 179.459
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Green fluorescent protein / superfolder green fluorescent protein


Mass: 25897.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059PIQ0, UniProt: P42212*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE THR 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE ...RESIDUE THR 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE CHROMOPHORE BF6 66.

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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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1M sodium malonate pH 4.0, 12% PEG 3350

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / % possible obs: 100 % / Redundancy: 12.4 % / Net I/σ(I): 15.8
Reflection shellResolution: 1.87→1.94 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.87→33.849 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.69
RfactorNum. reflection% reflection
Rfree0.2358 1073 5.13 %
Rwork0.2086 --
obs0.21 20924 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.87→33.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 0 66 1868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081841
X-RAY DIFFRACTIONf_angle_d1.0412489
X-RAY DIFFRACTIONf_dihedral_angle_d15.661098
X-RAY DIFFRACTIONf_chiral_restr0.059271
X-RAY DIFFRACTIONf_plane_restr0.005325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8695-1.95450.28441250.2082413X-RAY DIFFRACTION99
1.9545-2.05760.2661240.21532442X-RAY DIFFRACTION100
2.0576-2.18650.27251300.2232423X-RAY DIFFRACTION100
2.1865-2.35520.25171490.22552454X-RAY DIFFRACTION100
2.3552-2.59220.26381570.232432X-RAY DIFFRACTION100
2.5922-2.96710.29981220.24192494X-RAY DIFFRACTION100
2.9671-3.73740.21531320.21162524X-RAY DIFFRACTION99
3.7374-33.85490.17431340.16872669X-RAY DIFFRACTION98

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