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- PDB-4b5y: X-ray structure of the cyan fluorescent protein mTurquoise-GL (K2... -

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Basic information

Entry
Database: PDB / ID: 4b5y
TitleX-ray structure of the cyan fluorescent protein mTurquoise-GL (K206A mutant) in space group C222(1)
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / CFP / FRET / 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: 1.45 Å
Authorsvon Stetten, D. / Lelimousin, M. / Oost, K. / Noirclerc-Savoye, M. / Gadella, T.W.J. / Goedhart, J. / Royant, A.
Citation
Journal: To be Published
Title: Influence of the H148G Mutation on Fluorescence Properties of Cyan Fluorescent Proteins
Authors: von Stetten, D. / Lelimousin, M. / Oost, K. / Noirclerc-Savoye, M. / Gadella, T.W.J. / Goedhart, 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
DepositionAug 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Oct 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 1.3Dec 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 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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

Downloads & links

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Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)27,6221
Polymers27,6221
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.731, 92.481, 117.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2045-

HOH

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Components

#1: Protein GREEN FLUORESCENT PROTEIN / CYAN FLUORESCENT PROTEIN MTURQUOISE-GL


Mass: 27622.152 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CHROMOPHORE RESULTING FROM THE AUTOCATALYTIC CYCLISATION OF RESIDUES 65 TO 67
Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Plasmid: PQE60 / 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.: 172 / 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: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 6.5
Details: 35 MG/ML PROTEIN, 14% PEG8000, 100 MM MGCL2, 100 MM HEPES PH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 1, 2010 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.45→46.6 Å / Num. obs: 57436 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

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

2wso


Resolution: 1.45→38.42 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.988 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17878 2865 5 %RANDOM
Rwork0.14539 ---
obs0.1471 54420 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--1.16 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.45→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 0 172 2001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021909
X-RAY DIFFRACTIONr_bond_other_d0.0020.021290
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9762587
X-RAY DIFFRACTIONr_angle_other_deg0.9183.0013159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9325227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02625.43592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03515338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.128156
X-RAY DIFFRACTIONr_chiral_restr0.1050.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022086
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_restr3.53733199
X-RAY DIFFRACTIONr_sphericity_free26.186566
X-RAY DIFFRACTIONr_sphericity_bonded12.24953262
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 204 -
Rwork0.278 3875 -
obs--99.63 %

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