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- PDB-2q6p: The Chemical Control of Protein Folding: Engineering a Superfolde... -

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Basic information

Entry
Database: PDB / ID: 2q6p
TitleThe Chemical Control of Protein Folding: Engineering a Superfolder Green Fluorescent Protein
ComponentsGreen fluorescent protein mutant 3
KeywordsLUMINESCENT PROTEIN / GFP / Noncanonical amino acid / superfolder
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
Green fluorescent protein / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSteiner, T. / Hess, P. / Bae, J.H. / Wiltschi, B. / Moroder, L. / Budisa, N.
CitationJournal: Plos One / Year: 2008
Title: Synthetic biology of proteins: tuning GFPs folding and stability with fluoroproline.
Authors: Steiner, T. / Hess, P. / Bae, J.H. / Wiltschi, B. / Moroder, L. / Budisa, N.
History
DepositionJun 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE The residues THR 65, TYR 66 and GLY 67 constitute the chromophore CRO 66.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein mutant 3


Theoretical massNumber of molelcules
Total (without water)27,0911
Polymers27,0911
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.168, 62.556, 69.215
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 mutant 3


Mass: 27091.275 Da / Num. of mol.: 1 / Mutation: F64L,A72S,Q80R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93125, UniProt: P42212*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 20, 2004
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→46 Å / Num. all: 13465 / Num. obs: 12901 / % possible obs: 95.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 6.8 Å2
Reflection shellResolution: 2.1→2.17 Å / % possible all: 98

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMG
Resolution: 2.1→19.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 445648.094 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1330 10.3 %RANDOM
Rwork0.227 ---
all0.23 13465 --
obs0.227 12901 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.543 Å2 / ksol: 0.56 e/Å3
Displacement parametersBiso mean: 15.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.17 Å20 Å20 Å2
2---0.35 Å20 Å2
3---4.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 0 117 1923
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 213 10.4 %
Rwork0.227 1837 -
obs-2050 93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1gfp.pargfp.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3protein_rep.paramprotein.top
X-RAY DIFFRACTION4ion.paramion.top

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