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- PDB-2q57: X-ray structure of Cerulean GFP: A tryptophan-based chromophore u... -

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Basic information

Entry
Database: PDB / ID: 2q57
TitleX-ray structure of Cerulean GFP: A tryptophan-based chromophore useful for fluorescence lifetime imaging
ComponentsCerulean Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / BETA BARREL
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMalo, G.D.
CitationJournal: Biochemistry / Year: 2007
Title: X-ray structure of Cerulean GFP: a tryptophan-based chromophore useful for fluorescence lifetime imaging.
Authors: Malo, G.D. / Pouwels, L.J. / Wang, M. / Weichsel, A. / Montfort, W.R. / Rizzo, M.A. / Piston, D.W. / Wachter, R.M.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Non-polymer description
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 / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Residues SER 65, TYR 66 of the Green fluorescent protein sequence (UNP entry P42212) were ...SEQUENCE Residues SER 65, TYR 66 of the Green fluorescent protein sequence (UNP entry P42212) were mutated to THR 65, TRP 66 in the Cerulean Green fluorescent protein and then cyclized together with resuidue GLY 67 to form a chromophore CRF 66.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cerulean Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,7031
Polymers28,7031
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.232, 63.339, 69.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer and there is one monomer per assymetric unit.

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Components

#1: Protein Cerulean Green fluorescent protein


Mass: 28703.443 Da / Num. of mol.: 1
Mutation: F64L, S72A, Q80R, Y145A, N146I, H148D, M153T, V163A, H231L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pQE-9 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.973337 Å3/Da / Density % sol: 37.669037 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100mM sodium acetate, 19% PEG 4000, 1mM EDTA, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2006
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 15852 / % possible obs: 99.5 % / Observed criterion σ(I): 4 / Redundancy: 5.7 % / Biso Wilson estimate: 14.95 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 5.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 1.8 / Num. unique all: 13288 / Rsym value: 0.207 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ALSBEAMLINE 5.0.2data collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OXD

1oxd


Resolution: 2→19.92 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.871 / SU B: 4.155 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26206 791 5 %RANDOM
Rwork0.18806 ---
obs0.19172 15023 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.245 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.192 Å0.198 Å
Luzzati sigma a-0.121 Å
Refinement stepCycle: LAST / Resolution: 2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 0 149 1938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221832
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.9752482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0565224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20324.94185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66915305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.214157
X-RAY DIFFRACTIONr_chiral_restr0.1130.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021405
X-RAY DIFFRACTIONr_nbd_refined0.20.2743
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21206
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3390.218
X-RAY DIFFRACTIONr_mcbond_it1.1551.51157
X-RAY DIFFRACTIONr_mcangle_it1.78921806
X-RAY DIFFRACTIONr_scbond_it3.023834
X-RAY DIFFRACTIONr_scangle_it4.8244.5676
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 70 -
Rwork0.172 1071 -
obs-1071 98.45 %

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