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- PDB-8w97: De novo design protein -PK16 -

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Basic information

Entry
Database: PDB / ID: 8w97
TitleDe novo design protein -PK16
ComponentsDe novo design protein
KeywordsDE NOVO PROTEIN / De novo design protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionSep 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 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


Theoretical massNumber of molelcules
Total (without water)16,1061
Polymers16,1061
Non-polymers00
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)93.948, 93.948, 70.845
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein De novo design protein


Mass: 16105.732 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)
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: 5.6 Å3/Da / Density % sol: 78.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 20% w/v PEG 10000 0.1M Hepes ph7.5

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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: Apr 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→35.28 Å / Num. obs: 7519 / % possible obs: 72.75 % / Redundancy: 13.4 % / Biso Wilson estimate: 59.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.99
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 296 / CC1/2: 0.62

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Processing

Software
NameVersionClassification
PHENIXdev_4788refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→35.28 Å / SU ML: 0.1392 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.3409
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2547 303 5.02 %
Rwork0.2378 5728 -
obs0.2388 6031 72.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.04 Å2
Refinement stepCycle: LAST / Resolution: 2.9→35.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 0 0 1054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00981061
X-RAY DIFFRACTIONf_angle_d1.28821419
X-RAY DIFFRACTIONf_chiral_restr0.0669176
X-RAY DIFFRACTIONf_plane_restr0.0058171
X-RAY DIFFRACTIONf_dihedral_angle_d8.8335140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.630.28661100.31752099X-RAY DIFFRACTION55.41
3.7-35.280.24561930.21553629X-RAY DIFFRACTION93.84
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)
12.242166802360.5460122812380.9985997157132.590636077452.370100589772.293979337530.2299165323060.0966398881889-0.9941203177910.323167234880.2183005758420.3589594632160.8301625935880.0937496593757-0.1495072269980.424022677675-0.19129099635-0.1707357775230.0412790521048-0.04971910152810.47203143836840.8268670939-37.2583569405-17.2880086353
22.211400833160.00815854798382-0.4202762232040.535521929790.241412248720.4294248928160.1253219129180.652392174755-0.0129942285275-0.1429437116360.4858127922110.02112723420010.226684088129-0.3401481937470.1453866737690.608991693306-0.373170349286-0.3448325051881.578199077650.3531482031661.2147618280824.7153796115-30.9210530062-30.1234609912
31.66502135210.161753356421-0.6996197053252.0528275055-0.4259669869710.3572048702850.216951550780.5537455655760.136948037092-0.1078334539770.1859963541220.765961901567-0.145550838665-0.50679499260.1259721221790.1304061005210.1320767213580.02175188249340.825410308469-0.1393972504870.55713439158728.8148578048-25.2506074087-17.1722145212
41.46708873785-0.6933211756083.60111371687.13818760966-2.526478634148.949906623060.162858060345-1.354232025181.009681211131.06785233893-0.4281419849420.244582027836-0.524391959706-1.857847880260.09342960375410.298884970015-0.194768981944-0.0399188504110.801595276466-0.1947488245250.36920625557234.4176301362-28.8808397151-9.26291568134
52.154059993710.4361528534172.853745209541.34347062951.423185340884.33952106655-0.430950169134-0.190449402883-0.132811747158-0.2722075055550.1377408969030.992142622551-0.0262780649968-0.1225795291580.3742001351670.48794579402-0.357166447633-0.122062504231.252265069130.1401083171630.96779451668426.1322275122-32.8634813015-15.17987187
66.099460727010.6787176934580.6535671661289.67873203981.216302603854.673491457270.0592352675674-0.1851586155020.385959163559-0.351084863218-0.542000849750.313277446424-0.339015814502-0.2196209032260.4803651785050.3874428948090.06736869921610.005203680637350.188491811743-0.00574522011060.27337210737343.0100921729-28.678070707-7.74835024213
72.697151374920.5426486989381.298937622241.99366977538-1.546952208394.622427660740.4767189605240.501729386882-0.0169655349597-0.617939380753-0.3602734906230.248846894030.5058923797-0.808654387044-0.04966602770520.199831434223-0.0002771187788390.02555417399080.207201371269-0.02154035914070.32787482439638.9442074843-32.4655675527-24.7553004136
86.81179508391-1.99573683993-0.4855498058935.256781167411.435103774164.10628119756-0.132080238934-0.1439591829350.6286546578310.1841816693880.297228876583-1.03151128902-0.2852669355520.414777128655-0.1753219072130.3268372131850.2454726934430.06003729448360.127198460078-0.08137459956940.15035691984347.1555657382-28.2203856896-19.7373679021
91.60360156951-1.67755274860.9493308273592.22235788182-1.017078451842.41672879601-0.2138962192640.2258316438590.177391746892-0.1434860120560.258572465672-0.427222604060.222499098178-0.2022490536990.1813807009430.1244602966830.1451624793260.07955959877810.4428761306060.07291852816570.36023230107147.7919100976-28.3570860096-26.0212964388
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 24 )1 - 241 - 24
22chain 'A' and (resid 25 through 36 )25 - 3625 - 36
33chain 'A' and (resid 37 through 46 )37 - 4637 - 46
44chain 'A' and (resid 47 through 55 )47 - 5547 - 55
55chain 'A' and (resid 56 through 63 )56 - 6356 - 63
66chain 'A' and (resid 64 through 76 )64 - 7664 - 76
77chain 'A' and (resid 77 through 102 )77 - 10277 - 102
88chain 'A' and (resid 103 through 125 )103 - 125103 - 125
99chain 'A' and (resid 126 through 135 )126 - 135126 - 135

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