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- PDB-1qyo: Anaerobic precylization intermediate crystal structure for S65G Y... -

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Basic information

Entry
Database: PDB / ID: 1qyo
TitleAnaerobic precylization intermediate crystal structure for S65G Y66G GFP variant
Componentsgreen-fluorescent protein
KeywordsLUMINESCENT PROTEIN / beta barrel / chromophore / trapped intermediate
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
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBarondeau, D.P. / Putnam, C.D. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2003
Title: Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures.
Authors: Barondeau, D.P. / Putnam, C.D. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D.
History
DepositionSep 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)26,6341
Polymers26,6341
Non-polymers00
Water5,278293
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.937, 62.858, 71.781
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: 26633.918 Da / Num. of mol.: 1 / Mutation: F99S, M153T, V163A, F64L, S65G, Y66G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, Magnesium Chloride, Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 2, 2002
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 21947 / Num. obs: 21270 / % possible obs: 96.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.072 / Net I/σ(I): 20.2
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.366 / % possible all: 85.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ema

1ema


Resolution: 1.8→17.44 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 493845.43 / Data cutoff high rms absF: 493845.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.222 994 4.9 %RANDOM
Rwork0.197 ---
obs0.197 20447 93.8 %-
all-21947 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.5896 Å2 / ksol: 0.35782 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.18 Å20 Å20 Å2
2---0.81 Å20 Å2
3---6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→17.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 0 293 2150
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.62
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 148 5.1 %
Rwork0.289 2772 -
obs--81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.GFP.PARAMPROTEIN.GFP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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