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- PDB-11ce: Crystal structure of Zn5 with Zn -

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Basic information

Entry
Database: PDB / ID: 11ce
TitleCrystal structure of Zn5 with Zn
ComponentsThe protease-Zn (II) complex of Zn5
KeywordsDE NOVO PROTEIN / de novo design / metalloproteases / enzyme design / deep learning method
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 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

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Assembly

Deposited unit
A: The protease-Zn (II) complex of Zn5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9622
Polymers24,8971
Non-polymers651
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.804, 108.804, 89.074
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein The protease-Zn (II) complex of Zn5


Mass: 24897.006 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.08 Å3/Da / Density % sol: 69.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 21% PEG 350 MME, 0.5 M Magnesium chloride and 0.05 M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97905 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 3.41→64.73 Å / Num. obs: 5375 / % possible obs: 99.7 % / Redundancy: 10.1 % / Biso Wilson estimate: 85.23 Å2 / CC1/2: 0.961 / Rmerge(I) obs: 0.5 / Rpim(I) all: 0.17 / Net I/σ(I): 4.2
Reflection shellResolution: 3.41→3.68 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1113 / CC1/2: 0.479 / Rpim(I) all: 0.37 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.41→64.73 Å / SU ML: 0.1784 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 18.8296
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2447 280 5.21 %
Rwork0.2116 5094 -
obs0.2134 5374 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.46 Å2
Refinement stepCycle: LAST / Resolution: 3.41→64.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 1 7 1664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00161678
X-RAY DIFFRACTIONf_angle_d0.35632252
X-RAY DIFFRACTIONf_chiral_restr0.0333240
X-RAY DIFFRACTIONf_plane_restr0.0031299
X-RAY DIFFRACTIONf_dihedral_angle_d14.0931657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.41-4.290.27981380.23152540X-RAY DIFFRACTION99.48
4.29-64.730.22691420.20072554X-RAY DIFFRACTION99.93

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