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- PDB-11cr: Crystal structure of Zn5 -

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Basic information

Entry
Database: PDB / ID: 11cr
TitleCrystal structure of Zn5
ComponentsZn5
KeywordsDE NOVO PROTEIN / de novo design / metalloproteases / enzyme design / deep learning method
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.57 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: Zn5


Theoretical massNumber of molelcules
Total (without water)24,8971
Polymers24,8971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.332, 107.332, 89.351
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 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)
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: 3.98 Å3/Da / Density % sol: 69.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.05 M Glycine ph 9.0 and 55 % v/v PEG 400

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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: 3.57→64.42 Å / Num. obs: 4544 / % possible obs: 99.8 % / Redundancy: 10.8 % / Biso Wilson estimate: 122.34 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.381 / Rpim(I) all: 0.924 / Net I/σ(I): 3.3
Reflection shellResolution: 3.57→3.91 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.924 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1066 / CC1/2: 0.678 / Rpim(I) all: 0.323 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.57→64.42 Å / SU ML: 0.4186 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.9184
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2501 453 9.98 %
Rwork0.232 4088 -
obs0.2338 4541 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 130.09 Å2
Refinement stepCycle: LAST / Resolution: 3.57→64.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 0 0 1675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021697
X-RAY DIFFRACTIONf_angle_d0.39542277
X-RAY DIFFRACTIONf_chiral_restr0.0329243
X-RAY DIFFRACTIONf_plane_restr0.004302
X-RAY DIFFRACTIONf_dihedral_angle_d13.1191664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.57-4.090.31241470.29911355X-RAY DIFFRACTION99.67
4.09-5.150.28131520.24881371X-RAY DIFFRACTION100
5.15-64.420.21471540.19951362X-RAY DIFFRACTION99.67
Refinement TLS params.Method: refined / Origin x: -11.6549070076 Å / Origin y: 24.5253586297 Å / Origin z: -0.0437264612303 Å
111213212223313233
T1.14559231378 Å2-0.118662559027 Å20.0274337327688 Å2-1.1884938377 Å2-0.0175081177909 Å2--1.05438127942 Å2
L1.09282292883 °2-1.21716199659 °2-0.0470776852544 °2-2.48042374329 °2-0.683859932975 °2--0.728288731147 °2
S-0.15150835912 Å °0.0962909609896 Å °0.0193077244748 Å °-0.097970745116 Å °0.217208939397 Å °-0.0327369209386 Å °0.127889279229 Å °-0.0194776560401 Å °-0.0329132741743 Å °
Refinement TLS groupSelection details: all

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