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- PDB-5eju: Ensemble refinement of the Crystal Structure of the Reversibly ph... -

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Basic information

Entry
Database: PDB / ID: 5eju
TitleEnsemble refinement of the Crystal Structure of the Reversibly photoswitching chromoprotein Dathail, Ground State
ComponentsReversibly photoswitching protein Dathail
KeywordsFLUORESCENT PROTEIN / Ensemble refinement / GFP / photoswitching
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsClose, D.W. / Langan, P.S. / Bradbury, A.R.M.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Evolution and characterization of a new reversibly photoswitching chromogenic protein, Dathail.
Authors: Langan, P.S. / Close, D.W. / Coates, L. / Rocha, R.C. / Ghosh, K. / Kiss, C. / Waldo, G. / Freyer, J. / Kovalevsky, A. / Bradbury, A.R.
History
DepositionNov 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / citation / database_2 / entity / pdbx_struct_oper_list / pdbx_validate_main_chain_plane / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_polymer_linkage.auth_atom_id_1 / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reversibly photoswitching protein Dathail


Theoretical massNumber of molelcules
Total (without water)25,9031
Polymers25,9031
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.970, 81.090, 39.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Number of models47
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

22A-473-

HOH

38A-349-

HOH

49A-453-

HOH

510A-450-

HOH

615A-447-

HOH

716A-451-

HOH

817A-441-

HOH

918A-446-

HOH

1019A-406-

HOH

1120A-445-

HOH

1221A-445-

HOH

1322A-469-

HOH

1428A-464-

HOH

1529A-445-

HOH

1630A-463-

HOH

1731A-453-

HOH

1832A-461-

HOH

1939A-452-

HOH

2040A-464-

HOH

2141A-451-

HOH

2242A-442-

HOH

2343A-460-

HOH

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Components

#1: Protein Reversibly photoswitching protein Dathail


Mass: 25903.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium Chloride, 0.1M Bis-Tris:HCl pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.65→28.27 Å / Num. obs: 29380 / % possible obs: 97.69 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.04356 / Net I/σ(I): 18.08
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.2119 / Mean I/σ(I) obs: 4.09 / % possible all: 87.25

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Cootmodel building
HKL-3000data collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→28.27 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.47
RfactorNum. reflection% reflection
Rfree0.1936 1880 6.42 %
Rwork0.1515 --
obs0.1542 29293 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 0 165 1910
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.019
X-RAY DIFFRACTIONf_angle_d2.155
X-RAY DIFFRACTIONf_dihedral_angle_d19.58
X-RAY DIFFRACTIONf_chiral_restr0.126
X-RAY DIFFRACTIONf_plane_restr0.011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6501-1.69470.28051270.23171792X-RAY DIFFRACTION85
1.6947-1.74460.26091220.20292066X-RAY DIFFRACTION96
1.7446-1.80090.20761600.16932048X-RAY DIFFRACTION97
1.8009-1.86520.18031250.15052093X-RAY DIFFRACTION97
1.8652-1.93990.20331460.16232070X-RAY DIFFRACTION98
1.9399-2.02820.19581500.16832099X-RAY DIFFRACTION98
2.0282-2.13510.2061390.16022123X-RAY DIFFRACTION98
2.1351-2.26880.19871450.15292140X-RAY DIFFRACTION99
2.2688-2.44390.20541460.14342132X-RAY DIFFRACTION99
2.4439-2.68980.20131530.13912138X-RAY DIFFRACTION99
2.6898-3.07870.18051510.15422177X-RAY DIFFRACTION100
3.0787-3.87780.21641520.15752212X-RAY DIFFRACTION100
3.8778-28.270.16081640.13662323X-RAY DIFFRACTION100

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