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- PDB-7amu: Crystal structure of rsEGFP2 T204A in its fluorescent on-state -

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Basic information

Entry
Database: PDB / ID: 7amu
TitleCrystal structure of rsEGFP2 T204A in its fluorescent on-state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Enhanced GFP / Reversibly Photoswitchable Fluorescent Protein / Photoconvertible FP
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: 1.64 Å
AuthorsMoreno-Chicano, T. / Schlichting, I. / Hartmann, E. / Zala, N. / Colletier, J.-P. / Weik, M.
CitationJournal: To Be Published
Title: Crystal structure of rsEGFP2 in its fluorescent on-state at pH 8.0
Authors: Moreno-Chicano, T. / Schlichting, I. / Hartmann, E. / Zala, N. / Colletier, J.-P. / Weik, M.
History
DepositionOct 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_mod_residue / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_common_name / _struct_ref_seq_dif.details ..._entity_src_gen.gene_src_common_name / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.seq_num

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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)29,34310
Polymers28,5021
Non-polymers8419
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-44 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.269, 61.809, 70.846
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein


Mass: 28502.176 Da / Num. of mol.: 1 / Mutation: F64L, S65A, Q69L, V163S, A206K, H231L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P42212
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 11 / Details: Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→46.58 Å / Num. obs: 28151 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 29.06 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.047 / Χ2: 0.96 / Net I/σ(I): 14.3
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1356 / CC1/2: 0.596 / Rrim(I) all: 1.547 / Χ2: 0.85 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless0.7.2data scaling
REFMAC5.8.0258phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5o89

5o89


Resolution: 1.64→41.57 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.015 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 1402 5 %RANDOM
Rwork0.1687 ---
obs0.1715 26697 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.32 Å2 / Biso mean: 33.375 Å2 / Biso min: 18.66 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å20 Å2
2--1.62 Å20 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 1.64→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 51 174 2088
Biso mean--66.72 45.54 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132169
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171941
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.6552957
X-RAY DIFFRACTIONr_angle_other_deg1.3521.5934545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1715276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40824.167108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26115364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.874157
X-RAY DIFFRACTIONr_chiral_restr0.0710.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022488
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02437
LS refinement shellResolution: 1.64→1.681 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.317 100 -
Rwork0.348 1923 -
obs--98.88 %

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