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- PDB-11cp: Crystal structure of apo-TDPr3 -

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Basic information

Entry
Database: PDB / ID: 11cp
TitleCrystal structure of apo-TDPr3
Componentsdesigned metalloprotease TDPr3
KeywordsDE NOVO PROTEIN / de novo design / metalloproteases / enzyme design / deep learning method
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBera, A.K. / Chen, A. / Wu, K. / Kang, A. / Nguyen, H. / Baker, D.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Bill & Melinda Gates FoundationINV-043758 United States
CitationJournal: To Be Published
Title: Computational design of metalloproteases
Authors: Chen, A. / Wu, K. / Bera, A.K. / Baker, D.
History
DepositionFeb 17, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: designed metalloprotease TDPr3
B: designed metalloprotease TDPr3


Theoretical massNumber of molelcules
Total (without water)42,6582
Polymers42,6582
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-8 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.434, 80.434, 167.029
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 1 - 184 / Label seq-ID: 1 - 184

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.99559598135798, -0.015729184901687, 0.092418800285222), (-0.011433549076565, -0.99883757223294, -0.04682711021741), (0.093047922380594, 0.045564207862403, -0. ...NCS oper: (Code: given
Matrix: (0.99559598135798, -0.015729184901687, 0.092418800285222), (-0.011433549076565, -0.99883757223294, -0.04682711021741), (0.093047922380594, 0.045564207862403, -0.99461851335199)
Vector: -1.6460146601068, 2.8383649872041, 44.563515267435)

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Components

#1: Protein designed metalloprotease TDPr3


Mass: 21328.980 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.: 17 / 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: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.07 M Sodium acetate trihydrate pH 4.6, 5.6% w/v Polyethylene glycol 4,000, and 30% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→33.66 Å / Num. obs: 15099 / % possible obs: 95.5 % / Redundancy: 12 % / Biso Wilson estimate: 59.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.043 / Net I/σ(I): 12.6
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.144 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2038 / CC1/2: 0.798 / Rpim(I) all: 0.348 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
AutoPDdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→33.66 Å / SU ML: 0.2916 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9608
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.273 768 5.11 %
Rwork0.2291 14271 -
obs0.2314 15039 95.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.61 Å2
Refinement stepCycle: LAST / Resolution: 2.7→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 0 17 3021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373042
X-RAY DIFFRACTIONf_angle_d0.67864102
X-RAY DIFFRACTIONf_chiral_restr0.0396456
X-RAY DIFFRACTIONf_plane_restr0.0086548
X-RAY DIFFRACTIONf_dihedral_angle_d21.38021196
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.2519506214108 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.910.29781540.26892913X-RAY DIFFRACTION100
2.91-3.20.32571600.25192925X-RAY DIFFRACTION100
3.2-3.640.2861460.23392500X-RAY DIFFRACTION89.33
3.67-4.610.25081450.2042769X-RAY DIFFRACTION94.33
4.61-33.660.26191630.23133164X-RAY DIFFRACTION99.79
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)
12.9658330921768-1.79595893620490.692549877433953.7191451285386-1.05671474589414.9316671329524-0.1239802830205-0.0138362896057390.104665671356820.29391857752262-0.016379118301406-0.38675852762704-0.0817585573691560.111608915993290.154764428789490.41021642594299-0.064393355000349-0.00978696514091040.27352055696283-0.019629482854120.32268255152942-21.510979833965-2.57978496591637.255705680917
23.85132065776161.3808192449173-0.635514336511442.9795261189883-0.634683326477394.9248280728972-0.11002151256246-0.095805143506844-0.17051199832861-0.218392746176-0.0062508158500879-0.290700741434790.147531217293710.241757389009610.133183535996510.399293737707780.0532761473403540.0735305399039270.19308752687249-0.0425434758197120.31551068355262-19.578163803523.9169769571885.3901064426925
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 1 - 184 / Label seq-ID: 1 - 184

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain A and resseq 1:184)AA
22(chain B and resseq 1:184)BB

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