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- PDB-8kc1: De novo design protein -NX5 -

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Basic information

Entry
Database: PDB / ID: 8kc1
TitleDe novo design protein -NX5
ComponentsDe novo design protein -NX5
KeywordsDE NOVO PROTEIN / De novo design protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, S. / Liu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Methods / Year: 2024
Title: De novo protein design with a denoising diffusion network independent of pretrained structure prediction models.
Authors: Liu, Y. / Wang, S. / Dong, J. / Chen, L. / Wang, X. / Wang, L. / Li, F. / Wang, C. / Zhang, J. / Wang, Y. / Wei, S. / Chen, Q. / Liu, H.
History
DepositionAug 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo design protein -NX5


Theoretical massNumber of molelcules
Total (without water)9,5991
Polymers9,5991
Non-polymers00
Water93752
1
A: De novo design protein -NX5

A: De novo design protein -NX5


Theoretical massNumber of molelcules
Total (without water)19,1972
Polymers19,1972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area1530 Å2
ΔGint-11 kcal/mol
Surface area8470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.341, 45.072, 45.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-136-

HOH

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Components

#1: Protein De novo design protein -NX5


Mass: 9598.624 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.2M Imidazole malate pH7.0 25% w/v PEG4000

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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 PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→45.6 Å / Num. obs: 8756 / % possible obs: 97.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 33.26 Å2 / CC1/2: 0.996 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 501 / CC1/2: 0.838

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→32.06 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 441 5.05 %
Rwork0.2292 --
obs0.2302 8730 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms632 0 0 52 684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013642
X-RAY DIFFRACTIONf_angle_d1.403869
X-RAY DIFFRACTIONf_dihedral_angle_d5.56886
X-RAY DIFFRACTIONf_chiral_restr0.08899
X-RAY DIFFRACTIONf_plane_restr0.007115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-2.060.3351480.29062574X-RAY DIFFRACTION94
2.06-2.60.33771550.30222771X-RAY DIFFRACTION100
2.6-32.060.21061380.20262944X-RAY DIFFRACTION100
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)
15.77856.0157-5.77787.1767-4.96696.9069-0.2250.4470.1841-0.3456-0.1777-0.4489-0.41810.64820.29060.3108-0.1141-0.02340.48990.1740.387815.3686.80471.8262
24.13162.5964-2.88455.77791.31335.5063-0.35360.27130.3687-0.55990.19610.5318-0.6581.03650.07510.3406-0.1547-0.10520.42520.1330.38389.32638.82891.1525
34.8231-1.14690.50537.5720.39346.3353-0.2516-0.20870.368-0.38880.5484-0.1904-0.33440.2056-0.29920.2806-0.0969-0.04610.42020.00770.289421.319113.49756.7021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 82 )

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