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- PDB-4uts: Room temperature crystal structure of the fast switching M159T mu... -

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Basic information

Entry
Database: PDB / ID: 4uts
TitleRoom temperature crystal structure of the fast switching M159T mutant of fluorescent protein Dronpa
ComponentsFLUORESCENT PROTEIN DRONPA
KeywordsFLUORESCENT PROTEIN / PHOTOSWITCHING / PHOTOCHROMIC
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / metal ion binding / identical protein binding
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
Fluorescent protein Dronpa
Similarity search - Component
Biological speciesECHINOPHYLLIA SP. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsKaucikas, M. / Fitzpatrick, A. / Bryan, E. / Struve, A. / Henning, R. / Kosheleva, I. / Srajer, V. / van Thor, J.J.
CitationJournal: Proteins / Year: 2015
Title: Room Temperature Crystal Structure of the Fast Switching M159T Mutant of the Fluorescent Protein Dronpa.
Authors: Kaucikas, M. / Fitzpatrick, A. / Bryan, E. / Struve, A. / Henning, R. / Kosheleva, I. / Srajer, V. / Groenhof, G. / Van Thor, J.J.
History
DepositionJul 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 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 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn / struct_sheet
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_polymer_linkage.auth_atom_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_sheet.number_strands
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLUORESCENT PROTEIN DRONPA
B: FLUORESCENT PROTEIN DRONPA
C: FLUORESCENT PROTEIN DRONPA
D: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)98,0474
Polymers98,0474
Non-polymers00
Water4,360242
1
A: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)24,5121
Polymers24,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)24,5121
Polymers24,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)24,5121
Polymers24,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)24,5121
Polymers24,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.655, 111.140, 117.572
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
FLUORESCENT PROTEIN DRONPA


Mass: 24511.645 Da / Num. of mol.: 4 / Fragment: FLUORESCENT PROTEIN, RESIDUES 2-217 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ECHINOPHYLLIA SP. SC22 (invertebrata) / Plasmid: PRSET / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: Q5TLG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7.5
Details: 22 % (W/V) PEG (POLY[ETHYLENE GLYCOL]) MONOMETHYL ETHER 3350 AND 0.14 M MG(NO3)2, PH 7.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2013 / Details: BENT CONICAL SI-MIRROR (RH COATED)
RadiationMonochromator: BENT GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.04→55.82 Å / Num. obs: 810104 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.4
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.9 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z1O

2z1o


Resolution: 2.03→55.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.856 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21326 3241 5.1 %RANDOM
Rwork0.17153 ---
obs0.17368 60780 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.625 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å20 Å2
2---1.15 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.03→55.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6904 0 0 242 7146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197088
X-RAY DIFFRACTIONr_bond_other_d0.0050.026536
X-RAY DIFFRACTIONr_angle_refined_deg2.171.969572
X-RAY DIFFRACTIONr_angle_other_deg0.954315112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8145844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36824.483348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.645151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0671528
X-RAY DIFFRACTIONr_chiral_restr0.2950.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218016
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021668
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.029→2.082 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 179 -
Rwork0.222 3892 -
obs--86.23 %

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