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- PDB-8j98: A near-infrared fluorescent protein of de novo backbone design -

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Basic information

Entry
Database: PDB / ID: 8j98
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
Function / homologyChem-9UY / FORMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsHu, X. / Xu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: De novo backbone design for monomerization of near-infrared fluorescent protein
Authors: Hu, X. / Xu, Y.
History
DepositionMay 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: near-infrared fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1948
Polymers24,3311
Non-polymers8637
Water00
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)105.987, 105.987, 41.691
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein near-infrared fluorescent protein


Mass: 24331.281 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)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-9UY / 3-[5-[[(3~{R},4~{R})-3-ethenyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid / Billeverdin IXa, bound form


Mass: 586.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H38N4O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5 / Details: 3.5 M Sodium Formate, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 6001 / % possible obs: 95.67 % / Redundancy: 15 % / Biso Wilson estimate: 32.03 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.06
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 499 / CC1/2: 0.792

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.19.2_4158refinement
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→34.69 Å / SU ML: 0.1262 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.3046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2463 278 4.75 %
Rwork0.209 5577 -
obs0.211 5855 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.82 Å2
Refinement stepCycle: LAST / Resolution: 2.9→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1473 0 60 0 1533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00431561
X-RAY DIFFRACTIONf_angle_d0.63522095
X-RAY DIFFRACTIONf_chiral_restr0.0308220
X-RAY DIFFRACTIONf_plane_restr0.0035262
X-RAY DIFFRACTIONf_dihedral_angle_d16.4915601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.650.33021110.23022770X-RAY DIFFRACTION95.18
3.68-34.690.21041670.19482807X-RAY DIFFRACTION98.25

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