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- PDB-8ka7: De novo design protein -NB7 -

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Basic information

Entry
Database: PDB / ID: 8ka7
TitleDe novo design protein -NB7
ComponentsDe novo design protein -NB7
KeywordsDE NOVO PROTEIN / De novo design protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 -NB7


Theoretical massNumber of molelcules
Total (without water)13,0411
Polymers13,0411
Non-polymers00
Water1,20767
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)79.553, 79.553, 92.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-265-

HOH

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Components

#1: Protein De novo design protein -NB7


Mass: 13040.677 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.: 67 / 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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 20%w/v PEG4K, 20% iso-Propanole ,0.1M Sodium Citrate ,pH5.6

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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: 1.85→56.25 Å / Num. obs: 12836 / % possible obs: 99 % / Redundancy: 23.8 % / Biso Wilson estimate: 37.75 Å2 / CC1/2: 1 / Net I/σ(I): 39.3
Reflection shellResolution: 1.85→1.89 Å / Num. unique obs: 689 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→35.64 Å / SU ML: 0.2177 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2345 638 4.98 %
Rwork0.2189 12183 -
obs0.2197 12821 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.13 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 0 67 895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077837
X-RAY DIFFRACTIONf_angle_d0.99461139
X-RAY DIFFRACTIONf_chiral_restr0.0661137
X-RAY DIFFRACTIONf_plane_restr0.0066155
X-RAY DIFFRACTIONf_dihedral_angle_d14.6447310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.990.27441230.29472280X-RAY DIFFRACTION94.68
1.99-2.190.25821260.24942419X-RAY DIFFRACTION99.96
2.19-2.510.30781330.26362429X-RAY DIFFRACTION100
2.51-3.160.29671330.24662462X-RAY DIFFRACTION100
3.16-35.640.18421230.18982593X-RAY DIFFRACTION99.93
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)
13.22004399333-0.548690868456-0.6492203885495.401356506972.401254178973.39302420356-0.140907688183-0.3201540702710.368707436214-0.2974191075050.009033257983670.986692754575-0.250234114462-0.740065598820.001080116159470.3258708239140.033632788222-0.01037734729840.4682032090840.03630644024480.642602179731-5.84066029346.7130962714-15.3164691021
24.486752477641.282507267311.021625850512.987717342030.8313262084291.09640105272-0.0523847834993-0.2256710121680.09993477030940.2417887664070.04381973208290.2721046819980.1039109013610.0296554376705-0.008712106966150.260919402735-0.02451559152010.04369122115030.328702992461-0.002843504585180.2202049029496.893745896037.92653393504-7.77641661703
34.404054432762.32976556485-0.5835008509485.34094434115-0.2027262169724.86482423666-0.04087595404730.07414933985490.649917448470.06678038208710.105813671710.928716383585-0.285799762162-0.226206779945-0.01758281595610.251399892384-0.01836270253570.02928363162970.3012039771960.01694003085460.4291624376931.5020864999318.3299094005-13.2734936505
42.13069842188-0.5634025951410.7888812055181.48064669502-1.690381847495.23880803791-0.134708881510.1378920284780.6517917218680.0117764376612-0.339209078705-0.0977787818358-0.06517592691270.225695423140.5278452887780.460162555222-0.09443333183660.02483381157260.3901386672810.07450328353430.5669448234618.035417616325.7376975379-16.8393577327
58.72689871848-4.817649246925.354452552977.39521753018-4.536763811139.18515539342-0.472519955850.6836334959971.177625533950.4371351798150.15816686004-0.6542733632-0.9232477915710.9578020836980.3897246098810.35510650359-0.091598475697-0.05004637863910.3424503392750.01364730201230.50840193361411.783826360321.8753348555-13.0426170648
66.454761528330.4095467519061.586295981322.64951613984-0.4870923337164.01657414377-0.1457923679261.411871424890.499394138537-0.8761379839150.1929689786610.9188650330160.1310045465650.629645411549-0.1635392841690.398913124992-0.0426439464507-0.1330006605130.4766987419840.1280225674450.4965565503652.4811159250418.2982350903-22.0575293245
77.088900486780.9049166589341.178494442023.40927604767-0.7126738219583.47108333126-0.2150932954211.4409420016-0.349560922274-0.3918510014770.2914178640320.5640595131190.00296010158888-0.0545827032436-0.1530245453220.25461291414-0.0637695868735-0.04903175445040.4149235381220.003887870505870.2783315209085.787934763938.1478041508-17.434354873
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 11 )1 - 111 - 11
22chain 'A' and (resid 12 through 34 )12 - 3412 - 34
33chain 'A' and (resid 35 through 61 )35 - 6135 - 61
44chain 'A' and (resid 62 through 77 )62 - 7762 - 77
55chain 'A' and (resid 78 through 88 )78 - 8878 - 88
66chain 'A' and (resid 89 through 99 )89 - 9989 - 99
77chain 'A' and (resid 100 through 115 )100 - 115100 - 115

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