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- PDB-8y33: A near-infrared fluorescent protein of de novo backbone design -

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Basic information

Entry
Database: PDB / ID: 8y33
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 / homology:
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: 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
DepositionJan 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7232
Polymers21,1371
Non-polymers5871
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • 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.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
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: 21136.699 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-V8U / 3-[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-2-[[5-[(3-ethyl-4-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


Mass: 586.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H38N4O6 / 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: 3.2 Å3/Da / Density % sol: 61.57 %
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: 95.65 % / Redundancy: 15 % / Biso Wilson estimate: 30.28 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
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→34.69 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 278 4.75 %
Rwork0.2002 --
obs0.2026 5854 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 0 0 1516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021551
X-RAY DIFFRACTIONf_angle_d0.6942090
X-RAY DIFFRACTIONf_dihedral_angle_d11.136215
X-RAY DIFFRACTIONf_chiral_restr0.032218
X-RAY DIFFRACTIONf_plane_restr0.003263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.650.32361110.22242769X-RAY DIFFRACTION95
3.68-34.690.21031670.18542807X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7912-1.1891.14133.07-0.45131.12360.16640.44170.6335-0.4831-0.2042-0.1911-0.25430.2638-0.08080.2487-0.07310.01730.13630.01630.1599-18.373556.5301-0.9499
22.5416-1.06291.37690.9171-0.88923.55830.0002-0.0869-0.0220.03880.0279-0.0373-0.20930.2643-0.01930.132-0.0560.01990.12420.02630.1743-14.55253.264815.114
30.77221.4552-0.15113.4985-0.87253.4635-0.15290.0393-0.02810.37350.1374-0.122-0.301-0.0453-0.06690.11390.03150.07040.23460.03580.151-21.714549.06620.133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 165 )
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 214 )

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