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- PDB-6myc: Room-temperature structure of deuterated Tetdron (isomorph 2) -

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Basic information

Entry
Database: PDB / ID: 6myc
TitleRoom-temperature structure of deuterated Tetdron (isomorph 2)
ComponentsPhotoswitchable protein TetdronPhotoswitch
KeywordsFLUORESCENT PROTEIN / Tetdron / Photo-Switchable Protein / Beta-Barrel
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / identical protein binding / metal ion binding / Fluorescent protein Dronpa
Function and homology information
Biological speciesEchinophyllia sp. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.396 Å
AuthorsDajnowicz, S. / Kovalevsky, A.
CitationJournal: To Be Published
Title: Room-temperature in crystallo photo-induced deprotonation and tetramerization of photo-switchable protein Padron2.0
Authors: Dajnowicz, S. / Langan, P.S. / Weiss, K.L. / Ivanov, I.N. / Kovalevsky, A.
History
DepositionNov 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Structure summary / Category: entity / struct / struct_keywords
Item: _entity.pdbx_description / _struct.pdbx_descriptor ..._entity.pdbx_description / _struct.pdbx_descriptor / _struct.title / _struct_keywords.text
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photoswitchable protein Tetdron
B: Photoswitchable protein Tetdron
C: Photoswitchable protein Tetdron
D: Photoswitchable protein Tetdron
E: Photoswitchable protein Tetdron
F: Photoswitchable protein Tetdron
G: Photoswitchable protein Tetdron
H: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)203,6478
Polymers203,6478
Non-polymers00
Water4,720262
1
A: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,4561
Polymers25,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,4561
Polymers25,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,4561
Polymers25,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,4561
Polymers25,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,4561
Polymers25,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,4561
Polymers25,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,4561
Polymers25,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,4561
Polymers25,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.988, 138.075, 115.804
Angle α, β, γ (deg.)90.00, 104.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Photoswitchable protein Tetdron / Photoswitch


Mass: 25455.869 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TLG6*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 50 mM Tris pH 7.5, 0.15 M NaOAc, and 24% w/v polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.39→40 Å / Num. obs: 103458 / % possible obs: 89.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 42.6
Reflection shellResolution: 2.39→2.48 Å / Rmerge(I) obs: 0.63 / Num. unique obs: 3182 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.396→37.373 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.65
RfactorNum. reflection% reflection
Rfree0.2108 5210 5.04 %
Rwork0.1527 --
obs0.1556 103458 60.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.396→37.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13810 0 0 262 14072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814178
X-RAY DIFFRACTIONf_angle_d1.08319136
X-RAY DIFFRACTIONf_dihedral_angle_d25.4215206
X-RAY DIFFRACTIONf_chiral_restr0.0581951
X-RAY DIFFRACTIONf_plane_restr0.0062487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3963-2.42350.3793800.34261277X-RAY DIFFRACTION24
2.4235-2.4520.4814780.30191558X-RAY DIFFRACTION29
2.452-2.48190.3095880.26651684X-RAY DIFFRACTION31
2.4819-2.51330.3273830.2711817X-RAY DIFFRACTION33
2.5133-2.54640.28141150.27771887X-RAY DIFFRACTION35
2.5464-2.58130.30091170.28232016X-RAY DIFFRACTION37
2.5813-2.61810.3519920.27662133X-RAY DIFFRACTION39
2.6181-2.65720.3071300.26292240X-RAY DIFFRACTION41
2.6572-2.69870.33071350.24912472X-RAY DIFFRACTION45
2.6987-2.74290.27491440.24812550X-RAY DIFFRACTION48
2.7429-2.79020.25611250.23422706X-RAY DIFFRACTION49
2.7902-2.84090.29651600.23292864X-RAY DIFFRACTION53
2.8409-2.89560.29911420.22332960X-RAY DIFFRACTION54
2.8956-2.95460.25291730.22722992X-RAY DIFFRACTION55
2.9546-3.01880.30671690.223159X-RAY DIFFRACTION58
3.0188-3.0890.23671810.20033439X-RAY DIFFRACTION63
3.089-3.16630.22192090.19633672X-RAY DIFFRACTION67
3.1663-3.25180.23072080.17473912X-RAY DIFFRACTION72
3.2518-3.34740.24922090.17314085X-RAY DIFFRACTION75
3.3474-3.45540.21742280.16394352X-RAY DIFFRACTION79
3.4554-3.57880.20012180.15344375X-RAY DIFFRACTION82
3.5788-3.7220.22462440.14684563X-RAY DIFFRACTION83
3.722-3.89120.19852170.14014609X-RAY DIFFRACTION84
3.8912-4.09610.2012270.13744608X-RAY DIFFRACTION84
4.0961-4.35240.21262500.11884518X-RAY DIFFRACTION84
4.3524-4.68790.16062320.0974517X-RAY DIFFRACTION83
4.6879-5.15850.13212650.09654477X-RAY DIFFRACTION82
5.1585-5.90250.16942800.10894361X-RAY DIFFRACTION81
5.9025-7.42690.18442140.13214366X-RAY DIFFRACTION80
7.4269-37.37750.15791970.10374079X-RAY DIFFRACTION75

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