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- PDB-1oxd: Expansion of the Genetic Code Enables Design of a Novel "Gold" Cl... -

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Basic information

Entry
Database: PDB / ID: 1oxd
TitleExpansion of the Genetic Code Enables Design of a Novel "Gold" Class of Green Fluorescent Proteins
Componentscyan fluorescent protein cfp
KeywordsLUMINESCENT PROTEIN / green fluorescent protein / chromophore / amino acid incorporation / tryptophan / genetic code
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / :
Function and homology information
Biological speciescfp marker plasmid pWM1009 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsHyun Bae, J. / Rubini, M. / Jung, G. / Wiegand, G. / Seifert, M.H. / Azim, M.K. / Kim, J.S. / Zumbusch, A. / Holak, T.A. / Moroder, L. ...Hyun Bae, J. / Rubini, M. / Jung, G. / Wiegand, G. / Seifert, M.H. / Azim, M.K. / Kim, J.S. / Zumbusch, A. / Holak, T.A. / Moroder, L. / Huber, R. / Budisa, N.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Expansion of the Genetic Code Enables Design of a Novel "Gold" Class of Green Fluorescent Proteins
Authors: Hyun Bae, J. / Rubini, M. / Jung, G. / Wiegand, G. / Seifert, M.H. / Azim, M.K. / Kim, J.S. / Zumbusch, A. / Holak, T.A. / Moroder, L. / Huber, R. / Budisa, N.
History
DepositionApr 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 14, 2011Group: Non-polymer description
Revision 1.4Oct 27, 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 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cyan fluorescent protein cfp


Theoretical massNumber of molelcules
Total (without water)25,7981
Polymers25,7981
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.952, 62.768, 69.519
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 cyan fluorescent protein cfp


Mass: 25798.102 Da / Num. of mol.: 1 / Mutation: Q80R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) cfp marker plasmid pWM1009 (others) / Production host: Escherichia coli (E. coli) / References: GenBank: 11321072
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 65THR, 66TRP AND 67GLY ARE MODIFIED TO MAKE THE CHROMOPHORE CRF66

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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: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
119 mg/mlECFP1drop
314 %(w/v)PEG10001drop
40.1 MHEPES1reservoirpH7.5
55 %PEG80001reservoir
610 %ethylene gylcol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 11, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.15→7.98 Å / Num. all: 79530 / Num. obs: 73514 / % possible obs: 92.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 11 Å2
Reflection shellResolution: 1.15→1.22 Å / % possible all: 75.6
Reflection
*PLUS
Lowest resolution: 8 Å / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
Lowest resolution: 1.17 Å / % possible obs: 84 % / Rmerge(I) obs: 0.247

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→7.98 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 6988 10.1 %RANDOM
Rwork0.214 ---
all0.229 79530 --
obs0.214 69062 86.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.4172 Å2 / ksol: 0.613 e/Å3
Displacement parametersBiso mean: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å20 Å2
2---1.99 Å20 Å2
3---4.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.15→7.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 0 166 1966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.15→1.22 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 972 9.8 %
Rwork0.303 8936 -
obs--75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PRO_CFP.PARPRO_CFP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 8 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006055
X-RAY DIFFRACTIONc_angle_deg1.54226
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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