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- PDB-8ka6: De novo design protein -NA7 -

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Basic information

Entry
Database: PDB / ID: 8ka6
TitleDe novo design protein -NA7
ComponentsDe novo design protein -NA7
KeywordsDE NOVO PROTEIN / De novo design protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 2, 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

Downloads & links

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Assembly

Deposited unit
A: De novo design protein -NA7
B: De novo design protein -NA7


Theoretical massNumber of molelcules
Total (without water)33,1702
Polymers33,1702
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-3 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.800, 89.785, 93.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein De novo design protein -NA7


Mass: 16585.031 Da / Num. of mol.: 2
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.: 8 / 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 Å3/Da / Density % sol: 38.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 30% w/v PEG1500

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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: May 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→46.51 Å / Num. obs: 16298 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.999 / Net I/σ(I): 19.5
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 1304 / CC1/2: 0.806

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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: 2.2→30.09 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 713 5.03 %
Rwork0.2509 --
obs0.2522 14169 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→30.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 0 8 2107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022115
X-RAY DIFFRACTIONf_angle_d0.3562870
X-RAY DIFFRACTIONf_dihedral_angle_d13.869765
X-RAY DIFFRACTIONf_chiral_restr0.03360
X-RAY DIFFRACTIONf_plane_restr0.003375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.370.33731210.31592644X-RAY DIFFRACTION100
2.37-2.610.35761380.31212648X-RAY DIFFRACTION100
2.61-2.990.31231400.29322666X-RAY DIFFRACTION100
2.99-3.760.27571480.27712675X-RAY DIFFRACTION100
3.76-30.090.25191660.21682823X-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)
13.1027-0.30950.67067.645-2.03146.1584-0.0879-0.2747-0.1342-0.38020.39670.30520.2981-0.924-0.24040.43690.039-0.11410.693-0.09190.4376-12.4214-11.38377.4727
24.4586-6.20591.1788.6821-1.69080.368-0.4073-1.6687-0.21482.84171.3445-1.90781.52411.1572-1.13310.92190.4555-0.19970.99770.03470.6406-1.6477-14.315330.2597
37.49013.24781.27888.242-0.24070.3119-1.6929-1.28960.7367-0.3540.4012-0.7118-0.8607-0.42770.91891.02580.1879-0.2850.7183-0.31481.04734.3622-10.345223.879
41.85550.52350.01518.8708-2.94013.3526-0.21450.3711-0.2993-0.5819-0.0203-0.75950.26380.47970.29750.50460.0940.00330.6173-0.18710.4918-2.4312-11.47895.7727
56.1793-1.2357-0.8326.05770.9277.5294-0.59530.48080.1450.21830.64240.61430.2386-1.1819-0.08680.32020.0481-0.09870.71490.04360.3328-12.159511.90815.0743
66.08971.3207-4.13269.4288-1.49442.9358-0.27380.9387-0.318-0.5647-0.3743-1.90050.3031.01280.6950.63240.08380.00420.9569-0.02460.51716.28169.28411.315
72.49420.7633-1.70828.0772-2.48486.3006-0.0624-0.39440.09321.04230.0555-0.34840.17720.7965-0.0230.47910.092-0.11870.5866-0.11910.3842-3.053311.091118.3242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 147 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 61 )
6X-RAY DIFFRACTION6chain 'B' and (resid 62 through 91 )
7X-RAY DIFFRACTION7chain 'B' and (resid 92 through 149 )

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