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- PDB-9deh: The designed serine hydrolase known as win31 -

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Basic information

Entry
Database: PDB / ID: 9deh
TitleThe designed serine hydrolase known as win31
ComponentsWin31
KeywordsHYDROLASE / serine hydrolase / designed enzyme / helical / lit
Function / homologyL(+)-TARTARIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsPellock, S.J. / Lauko, A. / Bera, A.K.
Funding support United States, 4items
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
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: Win31
B: Win31
C: Win31
D: Win31
E: Win31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,86113
Polymers90,5285
Non-polymers1,3338
Water1,06359
1
A: Win31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6444
Polymers18,1061
Non-polymers5393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Win31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4503
Polymers18,1061
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Win31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2562
Polymers18,1061
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Win31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2562
Polymers18,1061
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Win31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2562
Polymers18,1061
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.400, 106.993, 116.659
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Win31


Mass: 18105.586 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M di-Ammonium tartrate and 20% (w/v) PEG 3350

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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: 0.97936 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.21→58.33 Å / Num. obs: 40598 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 39.04 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.284 / Rpim(I) all: 0.09 / Net I/σ(I): 6.4
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 11.4 % / Rmerge(I) obs: 3.183 / Num. unique obs: 5849 / CC1/2: 0.424 / Rpim(I) all: 1.024 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→58.33 Å / SU ML: 0.373 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.0838
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2711 2004 4.95 %
Rwork0.239 38453 -
obs0.2406 40457 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.99 Å2
Refinement stepCycle: LAST / Resolution: 2.21→58.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6204 0 83 59 6346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826359
X-RAY DIFFRACTIONf_angle_d0.72538555
X-RAY DIFFRACTIONf_chiral_restr0.0585975
X-RAY DIFFRACTIONf_plane_restr0.00441129
X-RAY DIFFRACTIONf_dihedral_angle_d14.7162463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.260.3871380.38012717X-RAY DIFFRACTION99.76
2.26-2.330.43551400.36552690X-RAY DIFFRACTION99.89
2.33-2.390.37861420.33932688X-RAY DIFFRACTION99.58
2.39-2.470.39451350.31932729X-RAY DIFFRACTION99.83
2.47-2.560.37941490.30822702X-RAY DIFFRACTION99.72
2.56-2.660.30611370.29492723X-RAY DIFFRACTION99.76
2.66-2.780.36521510.29322713X-RAY DIFFRACTION99.62
2.78-2.930.32581260.2922733X-RAY DIFFRACTION99.86
2.93-3.110.33831550.26652722X-RAY DIFFRACTION99.79
3.11-3.350.33061400.26612763X-RAY DIFFRACTION99.9
3.35-3.690.28521400.22932756X-RAY DIFFRACTION99.79
3.69-4.230.20221450.20012777X-RAY DIFFRACTION99.9
4.23-5.320.22451510.19072810X-RAY DIFFRACTION99.93
5.32-58.330.1831550.17382930X-RAY DIFFRACTION99.71

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