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- PDB-2ye0: X-ray structure of the cyan fluorescent protein mTurquoise (K206A... -

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Basic information

Entry
Database: PDB / ID: 2ye0
TitleX-ray structure of the cyan fluorescent protein mTurquoise (K206A mutant)
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / FRET DONOR
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: 1.47 Å
Authorsvon Stetten, D. / Goedhart, J. / Noirclerc-Savoye, M. / Lelimousin, M. / Joosen, L. / Hink, M.A. / van Weeren, L. / Gadella, T.W.J. / Royant, A.
Citation
Journal: Nat.Commun / Year: 2012
Title: Structure-Guided Evolution of Cyan Fluorescent Proteins Towards a Quantum Yield of 93%
Authors: Goedhart, J. / von Stetten, D. / Noirclerc-Savoye, M. / Lelimousin, M. / Joosen, L. / Hink, M.A. / van Weeren, L. / Gadella, T.W.J. / Royant, A.
#1: Journal: Nat.Methods / Year: 2010
Title: Bright Cyan Fluorescent Protein Variants Identified by Fluorescence Lifetime Screening.
Authors: Goedhart, J. / van Weeren, L. / Hink, M.A. / Vischer, N.O.E. / Jalink, K. / Gadella, T.W.J.J.
History
DepositionMar 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Other
Revision 1.2Sep 6, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Dec 20, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)27,6661
Polymers27,6661
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.984, 62.320, 70.366
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 / CYAN FLUORESCENT PROTEIN MTURQUOISE / CFP


Mass: 27666.162 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 64 TO LEU ENGINEERED RESIDUE IN CHAIN A, TYR 66 TO TRP ...ENGINEERED RESIDUE IN CHAIN A, PHE 64 TO LEU ENGINEERED RESIDUE IN CHAIN A, TYR 66 TO TRP ENGINEERED RESIDUE IN CHAIN A, SER 72 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASN 146 TO ILE ENGINEERED RESIDUE IN CHAIN A, HIS 148 TO ASP ENGINEERED RESIDUE IN CHAIN A, MET 153 TO THR ENGINEERED RESIDUE IN CHAIN A, VAL 163 TO ALA ENGINEERED RESIDUE IN CHAIN A, SER 175 TO GLY ENGINEERED RESIDUE IN CHAIN A, HIS 231 TO LEU
Has protein modificationY
Sequence detailsCHROMOPHORE RESULTING FROM THE AUTOCATALYTIC CYCLISATION OF RESIDUES 65 TO 67.

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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 Å3/Da / Density % sol: 39 %
Description: DATA WERE RECORDED USING THE ESRF HELICAL DATA COLLECTION PROCEDURE.
Crystal growpH: 6.75
Details: 16 MG/ML PROTEIN, 14% PEG8000, 100 MM MGCL2, 100 MM HEPES PH 6.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2010 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.47→46.7 Å / Num. obs: 38321 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.9
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WSO

2wso


Resolution: 1.47→41.29 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.509 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18495 1926 5 %RANDOM
Rwork0.1415 ---
obs0.14369 36342 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.835 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---0.53 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.47→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 0 166 1969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021872
X-RAY DIFFRACTIONr_bond_other_d0.0010.021259
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9712538
X-RAY DIFFRACTIONr_angle_other_deg0.8243.0013075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17325.32692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15215322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.677156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022062
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02365
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.81633131
X-RAY DIFFRACTIONr_sphericity_free27.246555
X-RAY DIFFRACTIONr_sphericity_bonded10.89553198
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 132 -
Rwork0.253 2484 -
obs--98.53 %

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