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- PDB-9r2k: De novo designed N30 protein fold -

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Basic information

Entry
Database: PDB / ID: 9r2k
TitleDe novo designed N30 protein fold
ComponentsN30
KeywordsDE NOVO PROTEIN / dark fold / de novo / unnatural
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsPacesa, M. / Miao, Y. / Georgeon, S. / Schmidt, J. / Correia, B.E.
Funding support1items
OrganizationGrant numberCountry
Swiss National Science Foundation
CitationJournal: To Be Published
Title: Reimagine accessibility of protein space with generative model
Authors: Miao, Y. / Pacesa, M. / Georgeon, S. / Schmidt, J. / Lu, T. / Huang, P. / Correia, B.E.
History
DepositionApr 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N30


Theoretical massNumber of molelcules
Total (without water)22,6581
Polymers22,6581
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9430 Å2
Unit cell
Length a, b, c (Å)75.600, 39.810, 54.630
Angle α, β, γ (deg.)90.000, 99.350, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein N30


Mass: 22658.311 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.: 65 / 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: 1.79 Å3/Da / Density % sol: 31.28 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 24.3 mg/ml; 0.1 M MES 6.5; 30 % v/v BCS PEG Smear Low

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.96→53.904 Å / Num. obs: 10853 / % possible obs: 92.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 25.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.161 / Net I/σ(I): 10.3
Reflection shellResolution: 1.961→1.995 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.584 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 574 / CC1/2: 0.347 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→53.9 Å / SU ML: 0.1976 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3867
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2525 537 4.95 %
Rwork0.1968 10316 -
obs0.1995 10853 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.2 Å2
Refinement stepCycle: LAST / Resolution: 1.96→53.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1509 0 0 65 1574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661531
X-RAY DIFFRACTIONf_angle_d0.85532044
X-RAY DIFFRACTIONf_chiral_restr0.0401213
X-RAY DIFFRACTIONf_plane_restr0.0076260
X-RAY DIFFRACTIONf_dihedral_angle_d16.9842622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.160.3051350.26442521X-RAY DIFFRACTION92.13
2.16-2.470.25971510.20562568X-RAY DIFFRACTION93.6
2.47-3.110.27441270.21122600X-RAY DIFFRACTION93.87
3.11-53.90.22561240.17342627X-RAY DIFFRACTION92.04
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)
11.31486214741-0.973140791555-1.118698955060.8749371234861.433593938991.92301259301-0.134877726134-0.0568508292211-0.01225687473810.05993750959250.0932931799211-0.0815798437883-0.03084933276510.192131972203-0.004274841428640.226732776353-0.00378636243988-0.003676863100790.2172645777550.01136445875810.21911476913923.76361254811.4439928902117.044118285
21.619471154250.0784379083330.02632459052791.04288589185-1.014068345591.289944785030.01773251846820.0831378556187-0.132000634740.0117863913330.0163136216620.1122676064960.1972866607650.09512706784466.45820984268E-60.1860620862740.006428950739630.0006566829163640.1503571180970.002289044088510.17583242648510.7948213687-1.8997520133614.7929461061
31.05737228010.1745500526630.05978206541141.77662343548-0.3658531690832.08564843008-0.01205250368830.1639043428220.0146567174851-0.07658295595640.0565192846329-0.0179073813119-0.0555056545716-0.2235588694440.0007289021410340.1181812423640.0240009814988-0.008792173505290.123835783125-0.01343291892560.12411278061912.05189841351.9097155001710.5427350287
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 57 )1 - 571 - 57
22chain 'A' and (resid 58 through 98 )58 - 9858 - 98
33chain 'A' and (resid 99 through 177 )99 - 17799 - 177

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