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- PDB-7dnb: Crystal structure of PhoCl barrel -

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Basic information

Entry
Database: PDB / ID: 7dnb
TitleCrystal structure of PhoCl barrel
ComponentsPhoCl Barrel
KeywordsFLUORESCENT PROTEIN / PhoCl / Photocleavable / GFP
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsWen, Y. / Lemieux, J.M.
CitationJournal: Chem Sci / Year: 2021
Title: Photocleavable proteins that undergo fast and efficient dissociation.
Authors: Lu, X. / Wen, Y. / Zhang, S. / Zhang, W. / Chen, Y. / Shen, Y. / Lemieux, M.J. / Campbell, R.E.
History
DepositionDec 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 23, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: PhoCl Barrel
A: PhoCl Barrel
B: PhoCl Barrel
D: PhoCl Barrel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,1285
Polymers110,1054
Non-polymers231
Water00
1
C: PhoCl Barrel


Theoretical massNumber of molelcules
Total (without water)27,5261
Polymers27,5261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PhoCl Barrel


Theoretical massNumber of molelcules
Total (without water)27,5261
Polymers27,5261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: PhoCl Barrel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5492
Polymers27,5261
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PhoCl Barrel


Theoretical massNumber of molelcules
Total (without water)27,5261
Polymers27,5261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.400, 119.640, 65.260
Angle α, β, γ (deg.)90.000, 107.660, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
PhoCl Barrel


Mass: 27526.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 1.57 Å3/Da / Density % sol: 21.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.81→43.11 Å / Num. obs: 16400 / % possible obs: 92.9 % / Redundancy: 2.7 % / CC1/2: 0.997 / Net I/σ(I): 8.54
Reflection shellResolution: 2.81→2.92 Å / Num. unique obs: 2688 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HQK

2hqk


Resolution: 2.81→43.11 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 36.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3354 1177 9.98 %
Rwork0.2749 10618 -
obs0.2808 11795 71.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.59 Å2 / Biso mean: 38.3944 Å2 / Biso min: 1.01 Å2
Refinement stepCycle: final / Resolution: 2.81→43.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4998 0 1 0 4999
Biso mean--2.16 --
Num. residues----675
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.81-2.940.5878150.44691501658
2.94-3.10.3596540.37251256627
3.1-3.290.43981410.33961250139168
3.29-3.540.36321980.29821754195294
3.55-3.90.32831980.27091754195295
3.9-4.460.29051860.24411733191994
4.47-5.620.29261910.23741743193493
5.63-43.110.34981940.2851722191691

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