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- PDB-11cy: Crystal structure of ZnO5_baseKO_ES -

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Basic information

Entry
Database: PDB / ID: 11cy
TitleCrystal structure of ZnO5_baseKO_ES
ComponentsZnO5_baseKO_ES
KeywordsDE NOVO PROTEIN / de novo design / metalloproteases / enzyme design / deep learning method
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 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: ZnO5_baseKO_ES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8482
Polymers23,7831
Non-polymers651
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.861, 107.861, 88.885
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 ZnO5_baseKO_ES


Mass: 23782.795 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.: 3 / 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: 4.18 Å3/Da / Density % sol: 70.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium chloride and 40% (v/v) MPD

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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: 2.77→64.39 Å / Num. obs: 9789 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 83.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.034 / Net I/σ(I): 15
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.058 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1413 / CC1/2: 0.784 / Rpim(I) all: 0.354 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→41.34 Å / SU ML: 0.442 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 30.8575
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2541 509 5.2 %
Rwork0.2165 9273 -
obs0.2186 9782 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.63 Å2
Refinement stepCycle: LAST / Resolution: 2.77→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 1 3 1666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271684
X-RAY DIFFRACTIONf_angle_d0.43922260
X-RAY DIFFRACTIONf_chiral_restr0.0336241
X-RAY DIFFRACTIONf_plane_restr0.0044300
X-RAY DIFFRACTIONf_dihedral_angle_d22.5154659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-3.050.37081060.28472320X-RAY DIFFRACTION99.96
3.05-3.490.31411280.26432331X-RAY DIFFRACTION99.96
3.49-4.390.26171370.21962303X-RAY DIFFRACTION99.84
4.4-41.340.22471380.19232319X-RAY DIFFRACTION99.84
Refinement TLS params.Method: refined / Origin x: 38.7268259123 Å / Origin y: -8.71107200391 Å / Origin z: 1.86088160857 Å
111213212223313233
T0.665067267471 Å20.0146188509646 Å2-0.00652098351092 Å2-0.751659235407 Å20.0210896409351 Å2--0.689668589396 Å2
L1.0998522021 °2-0.40459313633 °2-0.971990203713 °2-1.26377522838 °20.615292633799 °2--1.23176474611 °2
S0.0599422763948 Å °-0.0710371021797 Å °-0.0449379668694 Å °-0.0537206592062 Å °0.0211656632 Å °-0.00835547328866 Å °0.0228986098346 Å °-0.00207745862805 Å °-6.50218149903E-5 Å °
Refinement TLS groupSelection details: all

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