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- PDB-8j1x: A near-infrared fluorescent protein of de novo backbone design -

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Basic information

Entry
Database: PDB / ID: 8j1x
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: 2.25 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

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Assembly

Deposited unit
A: near-infrared fluorescent protein


Theoretical massNumber of molelcules
Total (without water)24,3311
Polymers24,3311
Non-polymers00
Water91951
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)64.330, 50.545, 66.651
Angle α, β, γ (deg.)90.000, 112.379, 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-308-

HOH

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Components

#1: Protein near-infrared fluorescent protein


Mass: 24331.281 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.: 51 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350

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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: Jan 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 9424 / % possible obs: 99.18 % / Redundancy: 6.3 % / Biso Wilson estimate: 37.98 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.17
Reflection shellResolution: 2.25→2.334 Å / Num. unique obs: 869 / CC1/2: 0.921

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.19.2_4158refinement
Aimlessdata scaling
MOLREPphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: SAD / Resolution: 2.25→38.52 Å / SU ML: 0.1929 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1637
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2141 461 4.9 %
Rwork0.1959 8954 -
obs0.1968 9415 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.9 Å2
Refinement stepCycle: LAST / Resolution: 2.25→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 0 51 1440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081426
X-RAY DIFFRACTIONf_angle_d1.01391915
X-RAY DIFFRACTIONf_chiral_restr0.0552209
X-RAY DIFFRACTIONf_plane_restr0.0089243
X-RAY DIFFRACTIONf_dihedral_angle_d15.5145552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.580.26661470.23342931X-RAY DIFFRACTION97.84
2.58-3.250.24171540.22742979X-RAY DIFFRACTION99.94
3.25-38.520.19041600.17493044X-RAY DIFFRACTION99.78

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