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- PDB-11cm: Crystal structure of the protease -Zn(II) - substrate complex of ZnO7 -

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Basic information

Entry
Database: PDB / ID: 11cm
TitleCrystal structure of the protease -Zn(II) - substrate complex of ZnO7
Components
  • ZnO7
  • ZnO7 substrate
KeywordsDE NOVO PROTEIN / de novo design / metalloproteases / enzyme design / deep learning method
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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: ZnO7
B: ZnO7 substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3203
Polymers22,2542
Non-polymers651
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-51 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.510, 66.510, 80.475
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein ZnO7


Mass: 21048.791 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: Protein/peptide ZnO7 substrate


Mass: 1205.493 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)
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.04 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.65 M Imidazole pH 7.0, and 35% 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: Jan 30, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.37→33.26 Å / Num. obs: 8753 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 30.94 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.65 / Rpim(I) all: 0.15 / Net I/σ(I): 4.3
Reflection shellResolution: 2.37→2.5 Å / Redundancy: 20 % / Rmerge(I) obs: 3.36 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1240 / CC1/2: 0.494 / Rpim(I) all: 0.78 / % 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: 2.37→33.26 Å / SU ML: 0.3426 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4285
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2867 869 9.95 %
Rwork0.2301 7863 -
obs0.2356 8732 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.36 Å2
Refinement stepCycle: LAST / Resolution: 2.37→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1435 0 1 44 1480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241476
X-RAY DIFFRACTIONf_angle_d0.45611995
X-RAY DIFFRACTIONf_chiral_restr0.0363234
X-RAY DIFFRACTIONf_plane_restr0.0054261
X-RAY DIFFRACTIONf_dihedral_angle_d16.5562590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.520.35071410.30671279X-RAY DIFFRACTION100
2.52-2.710.34031430.26741279X-RAY DIFFRACTION100
2.71-2.980.29371470.271305X-RAY DIFFRACTION100
2.99-3.410.32251380.23261290X-RAY DIFFRACTION100
3.42-4.30.27421450.20681323X-RAY DIFFRACTION100
4.3-33.260.24231550.20071387X-RAY DIFFRACTION100

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