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- PDB-5n9o: EGFP(enhanced green fluorescent protein) mutant - L232H -

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Basic information

Entry
Database: PDB / ID: 5n9o
TitleEGFP(enhanced green fluorescent protein) mutant - L232H
ComponentsGreen fluorescent protein
KeywordsCalcium binding protein / green fluorescent protein
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
3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsKachalova, G.S. / Popov, A.P. / Simanovskaya, A.A. / Krukova, M.V. / Lipkin, A.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research13-04-12084 Russian Federation
CitationJournal: To Be Published
Title: Structure of EGFP(enhanced green fluorescent protein) mutant - L232H at 0.153 nm
Authors: Kachalova, G.S. / Popov, A.P. / Simanovskaya, A.A. / Lipkin, A.V.
History
DepositionFeb 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5143
Polymers26,9811
Non-polymers5332
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint2 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.595, 67.931, 47.266
Angle α, β, γ (deg.)90.00, 118.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 26981.432 Da / Num. of mol.: 1 / Mutation: L232H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pHis-p1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212
#2: Chemical ChemComp-AE4 / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL


Mass: 266.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.21 Å3/Da / Density % sol: 44.3 % / Description: thick needle like
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2-propanol , MES monohydrate, PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2015 / Details: bent cylindrical mirrors
RadiationMonochromator: Single crystal. Crystal Type, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.53→41.48 Å / Num. obs: 34978 / % possible obs: 98.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.048 / Χ2: 0.997 / Net I/av σ(I): 6.8 / Net I/σ(I): 8.6
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3431 / CC1/2: 0.589 / Rpim(I) all: 0.38 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L12

4l12


Resolution: 1.53→12.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.761 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.086
RfactorNum. reflection% reflectionSelection details
Rfree0.21146 1733 5 %RANDOM
Rwork0.16721 ---
obs0.16948 33171 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20.08 Å2
2---0.01 Å20 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.53→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 36 293 2207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192021
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5091.9752727
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9175246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03525.36197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39615341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.577156
X-RAY DIFFRACTIONr_chiral_restr0.170.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211536
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2061.74968
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3052.611220
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.662.1161052
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.44235.518867
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 132 -
Rwork0.26 2384 -
obs--99.41 %

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