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- PDB-9def: The designed serine hydrolase known as win -

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Basic information

Entry
Database: PDB / ID: 9def
TitleThe designed serine hydrolase known as win
ComponentsWin
KeywordsHYDROLASE / serine hydrolase / designed enzyme / helical / lit
Function / homologyACETIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPellock, S.J. / Lauko, A. / Bera, A.K.
Funding support United States, 5items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Defense Advanced Research Projects Agency (DARPA) United States
Defense Threat Reduction Agency (DTRA) United States
Other private
CitationJournal: Science / Year: 2025
Title: Computational design of serine hydrolases.
Authors: Lauko, A. / Pellock, S.J. / Sumida, K.H. / Anishchenko, I. / Juergens, D. / Ahern, W. / Jeung, J. / Shida, A.F. / Hunt, A. / Kalvet, I. / Norn, C. / Humphreys, I.R. / Jamieson, C. / Krishna, ...Authors: Lauko, A. / Pellock, S.J. / Sumida, K.H. / Anishchenko, I. / Juergens, D. / Ahern, W. / Jeung, J. / Shida, A.F. / Hunt, A. / Kalvet, I. / Norn, C. / Humphreys, I.R. / Jamieson, C. / Krishna, R. / Kipnis, Y. / Kang, A. / Brackenbrough, E. / Bera, A.K. / Sankaran, B. / Houk, K.N. / Baker, D.
History
DepositionAug 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 30, 2025Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Win
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3673
Polymers18,2711
Non-polymers962
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.157, 46.019, 92.941
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-326-

HOH

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Components

#1: Protein Win


Mass: 18271.186 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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.82 Å3/Da / Density % sol: 32.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium acetate pH 4.6, 8% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.75→46.02 Å / Num. obs: 14105 / % possible obs: 99.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.028 / Net I/σ(I): 14
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.274 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 749 / CC1/2: 0.752 / Rpim(I) all: 0.402 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.02 Å / SU ML: 0.2455 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.0269
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2685 1406 10 %
Rwork0.2383 12651 -
obs0.2414 14057 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.85 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 5 64 1263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911232
X-RAY DIFFRACTIONf_angle_d0.8491666
X-RAY DIFFRACTIONf_chiral_restr0.06184
X-RAY DIFFRACTIONf_plane_restr0.0104232
X-RAY DIFFRACTIONf_dihedral_angle_d14.1021475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.36051370.32371229X-RAY DIFFRACTION99.71
1.81-1.890.35741370.29771231X-RAY DIFFRACTION99.78
1.89-1.970.29551360.28131245X-RAY DIFFRACTION99.78
1.97-2.070.30621410.25391252X-RAY DIFFRACTION99.57
2.07-2.20.27761380.23631241X-RAY DIFFRACTION99.35
2.21-2.370.32061380.2431241X-RAY DIFFRACTION99.49
2.38-2.610.28041400.24371267X-RAY DIFFRACTION99.93
2.61-2.990.29291420.25931269X-RAY DIFFRACTION99.65
2.99-3.770.24181440.23231299X-RAY DIFFRACTION100
3.77-46.020.23891530.21371377X-RAY DIFFRACTION99.61

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