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- PDB-5ebj: Joint X-ray/neutron structure of reversibly photoswitching chromo... -

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Basic information

Entry
Database: PDB / ID: 5ebj
TitleJoint X-ray/neutron structure of reversibly photoswitching chromogenic protein, Dathail
Componentsphotoswitching chromogenic protein
KeywordsFLUORESCENT PROTEIN / photoswitching chromogenic protein
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / DEUTERATED WATER
Function and homology information
Biological speciessynthetic construct (others)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKovalevsky, A.Y. / Langan, P.S. / Bradbury, A.R.M.
Citation
Journal: 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.
#1: Journal: Acta Cryst. / Year: 2009
Title: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules
Authors: Adams, P.D. / Mustyakimov, M. / Afonine, P.V. / Langan, P.
History
DepositionOct 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Apr 25, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type / _pdbx_struct_oper_list.symmetry_operation / _software.name
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 / diffrn_radiation_wavelength / pdbx_validate_torsion / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _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: photoswitching chromogenic protein


Theoretical massNumber of molelcules
Total (without water)25,9031
Polymers25,9031
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint13 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.209, 82.049, 40.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein photoswitching chromogenic protein


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: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Magnesium Chloride, 0.1M Bis-Tris:HCl pH 6.5, 25% PEG 3350

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORORNL Spallation Neutron Source MANDI12.0-4.0
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDateDetails
ORNL1ANGER CAMERASep 23, 2014COLLIMATORS
RIGAKU RAXIS IV++2IMAGE PLATEJan 13, 2014OSMIC VARIMAX
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
31.541
Reflection

Entry-ID: 5EBJ / Observed criterion σ(F): 2.5

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.5-40615863.61.40.31713.9
2.1-401527396.63.80.05225.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.560.80.2632.2147.9
2.1-2.183.60.5842.22100

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Processing

Software
NameVersionClassification
nCNS1.0.0refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Mantiddata reduction
SHELXPREPdata scaling
Refinement

Biso max: 90.97 Å2 / Biso mean: 43.44 Å2 / Biso min: 15.06 Å2 / % reflection Rfree: 5 % / R Free selection details: RANDOM / Cross valid method: FREE R-VALUE / σ(F): 2.5 / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: CNS bulk solvent model used

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)Diffraction-IDBsol (Å2)ksol (e/Å3)
2.5-40NEUTRON DIFFRACTION0.3440.30527454049281565260174.58750.726293
2.1-40X-RAY DIFFRACTION0.2530.2354899518157781187875.2256.95240.335146
Refine analyze
Refine-ID#notag 0
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.560.49
Luzzati d res low-5
Luzzati sigma a0.71.12
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.30.27
Luzzati d res low-5
Luzzati sigma a0.130.16
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 0 92 1838
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.01
NEUTRON DIFFRACTIONx_angle_deg1.3
NEUTRON DIFFRACTIONx_torsion_deg17.3
NEUTRON DIFFRACTIONx_torsion_impr_deg0.97
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree error% reflection obs (%)Redundancy reflection all
2.5-2.610.466163.30.405475NEUTRON DIFFRACTION0.06643.8
2.1-2.20.282297.20.2421926X-RAY DIFFRACTION0.052213.6

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