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- PDB-8j1w: A near-infrared fluorescent protein of de novo backbone design -

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Basic information

Entry
Database: PDB / ID: 8j1w
TitleA near-infrared fluorescent protein of de novo backbone design
Componentsnear-infrared fluorescent protein
KeywordsDE NOVO PROTEIN / De novo backbone design / monomerization / near-infrared fluorescent protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsHu, X. / Xu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Synth Biol / Year: 2024
Title: Using Protein Design and Directed Evolution to Monomerize a Bright Near-Infrared Fluorescent Protein.
Authors: Hu, X. / Xu, Y. / Yi, J. / Wang, C. / Zhu, Z. / Yue, T. / Zhang, H. / Wang, X. / Wu, F. / Xue, L. / Bai, L. / Liu, H. / Chen, Q.
History
DepositionApr 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: near-infrared fluorescent protein


Theoretical massNumber of molelcules
Total (without water)24,2861
Polymers24,2861
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.869, 50.138, 66.640
Angle α, β, γ (deg.)90.000, 111.431, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-356-

HOH

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Components

#1: Protein near-infrared fluorescent protein


Mass: 24286.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 20% PEG 3350, 0.2 M K dihydrogen Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 14068 / % possible obs: 97.22 % / Redundancy: 6.7 % / Biso Wilson estimate: 35.55 Å2 / CC1/2: 1 / Net I/σ(I): 21.37
Reflection shellResolution: 1.95→2.019 Å / Num. unique obs: 1345 / CC1/2: 0.928

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.19.2_4158refinement
AutoSolphasing
Aimlessdata scaling
PHENIX1.19.2_4158model building
RefinementMethod to determine structure: SAD / Resolution: 1.95→27.48 Å / SU ML: 0.2032 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.5098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2403 711 5.06 %
Rwork0.1866 13339 -
obs0.1892 14050 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.08 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 0 91 1486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641420
X-RAY DIFFRACTIONf_angle_d0.82341907
X-RAY DIFFRACTIONf_chiral_restr0.0462211
X-RAY DIFFRACTIONf_plane_restr0.0053240
X-RAY DIFFRACTIONf_dihedral_angle_d14.1267546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.10.30811470.25662569X-RAY DIFFRACTION95.3
2.1-2.310.26051310.2112660X-RAY DIFFRACTION97.11
2.31-2.650.22241480.20262688X-RAY DIFFRACTION98.4
2.65-3.330.24851420.2052688X-RAY DIFFRACTION97.86
3.33-27.480.22881430.16272734X-RAY DIFFRACTION97.69

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