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- PDB-6myb: Room-temperature structure of deuterated Tetdron (isomorph 1) -

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Basic information

Entry
Database: PDB / ID: 6myb
TitleRoom-temperature structure of deuterated Tetdron (isomorph 1)
ComponentsPhotoswitchable protein Tetdron
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 / Resolution: 1.899 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
Revision 2.1Oct 23, 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: 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
Water14,016778
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)71.623, 129.573, 98.564
Angle α, β, γ (deg.)90.00, 105.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Photoswitchable protein Tetdron


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


Mass: 18.015 Da / Num. of mol.: 778 / 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: 2.17 Å3/Da / Density % sol: 43.33 %
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: 1.89→40 Å / Num. obs: 116819 / % possible obs: 93.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 1.89→1.97 Å / Rmerge(I) obs: 0.388 / Num. unique obs: 4552

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 1.899→35.627 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.73
RfactorNum. reflection% reflection
Rfree0.2501 5905 5.05 %
Rwork0.199 --
obs0.2016 116819 85.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.899→35.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13880 0 0 778 14658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714256
X-RAY DIFFRACTIONf_angle_d1.00319238
X-RAY DIFFRACTIONf_dihedral_angle_d22.7965246
X-RAY DIFFRACTIONf_chiral_restr0.0611962
X-RAY DIFFRACTIONf_plane_restr0.0062498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8994-1.9210.30151380.24352440X-RAY DIFFRACTION57
1.921-1.94360.33041410.26192675X-RAY DIFFRACTION63
1.9436-1.96730.30441760.25352837X-RAY DIFFRACTION67
1.9673-1.99220.33871630.25063122X-RAY DIFFRACTION72
1.9922-2.01840.3041880.2533122X-RAY DIFFRACTION74
2.0184-2.04610.30382030.24473349X-RAY DIFFRACTION78
2.0461-2.07530.31641920.2413463X-RAY DIFFRACTION81
2.0753-2.10630.32111750.23253688X-RAY DIFFRACTION84
2.1063-2.13920.28632050.23163801X-RAY DIFFRACTION89
2.1392-2.17430.32162000.2263951X-RAY DIFFRACTION92
2.1743-2.21170.29612200.20994022X-RAY DIFFRACTION94
2.2117-2.2520.25222310.21044111X-RAY DIFFRACTION95
2.252-2.29530.28032170.21024046X-RAY DIFFRACTION94
2.2953-2.34210.27322320.21244024X-RAY DIFFRACTION94
2.3421-2.3930.27422060.22014105X-RAY DIFFRACTION95
2.393-2.44870.2952080.21594015X-RAY DIFFRACTION94
2.4487-2.50990.28911950.21953944X-RAY DIFFRACTION91
2.5099-2.57770.25811730.20933621X-RAY DIFFRACTION84
2.5777-2.65360.30481710.22153331X-RAY DIFFRACTION77
2.6536-2.73920.28082010.20114017X-RAY DIFFRACTION93
2.7392-2.8370.25372360.19564128X-RAY DIFFRACTION96
2.837-2.95060.27192030.20914149X-RAY DIFFRACTION96
2.9506-3.08480.28422040.20544168X-RAY DIFFRACTION96
3.0848-3.24730.23472360.18834080X-RAY DIFFRACTION95
3.2473-3.45060.21122250.17844050X-RAY DIFFRACTION94
3.4506-3.71680.20331940.16823963X-RAY DIFFRACTION91
3.7168-4.09040.19742080.16993839X-RAY DIFFRACTION89
4.0904-4.68110.18641800.16263617X-RAY DIFFRACTION83
4.6811-5.89340.2021730.16573314X-RAY DIFFRACTION76
5.8934-35.63280.20562110.19173922X-RAY DIFFRACTION89

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