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- PDB-38rr: Cryo-EM structure of Sr01-080, a denovo designed borneol dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 38rr
TitleCryo-EM structure of Sr01-080, a denovo designed borneol dehydrogenase
ComponentsSr01-080
KeywordsOXIDOREDUCTASE / Dehydrogenase / De novo designed protein / borneol dehydrogenase
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsMiles, U. / McShan, A. / McManus, C. / Kamerlin, S.C.L. / Di Geronimo Quintero, B.
Funding support United States, 2items
OrganizationGrant numberCountry
Other government United States
Other private United States
CitationJournal: To Be Published
Title: Full-Atom MPNN Based Redesign of Plant Dehydrogenase Enables Thermostability Enhancement Without Loss of Stereoselectivity
Authors: Miles, U. / McShan, A. / McManus, C. / Kamerlin, S.C.L. / Di Geronimo Quintero, B.
History
DepositionSep 15, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sr01-080
B: Sr01-080
C: Sr01-080
D: Sr01-080


Theoretical massNumber of molelcules
Total (without water)112,8644
Polymers112,8644
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, gel filtration, Tetramer observed
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_4ens_1chain "D"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 1 - 259 / Label seq-ID: 9 - 267

Dom-IDAuth asym-IDLabel asym-ID
d_1CC
d_2BB
d_3AA
d_4DD

NCS oper:
IDCodeMatrixVector
1given(-0.99999999944075, -2.2824500019624E-5, -2.4444570847377E-5), (-2.2826678003613E-5, 0.99999999576986, 8.9102311849304E-5), (2.4442537028255E-5, 8.9102869787821E-5, -0.99999999573162)294.14473110058, -0.015962109869122, 294.12428539444
2given(0.99999950631199, 0.00085907116452305, 0.00049937212415975), (0.00085899645638682, -0.99999961984255, 0.00014979937117376), (0.00049950062263995, -0.00014937033833454, -0.99999986409381)-0.17751420360653, 294.02876712143, 294.09981652369
3given(-0.99999994147779, -0.00029399993988168, -0.0001749527023543), (0.00029402942515337, -0.999999942572, -0.00016853096792069), (-0.00017490314421268, -0.00016858239930039, 0.99999997049443)294.19987143587, 294.13503441939, 0.048009756655858

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Components

#1: Protein
Sr01-080


Mass: 28216.090 Da / Num. of mol.: 4
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: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 01_80 / Type: CELL / Details: Tetrameric complex of 4 01_80 units / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 125 mM NaCl, 10 mM Tris HCl (pH = 8.0)
Buffer component
IDConc.NameFormulaBuffer-ID
1125 mMSodium ChlorideNaCl1
220 mMTrisC4H11NO31
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This samples was monodisperse
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 100000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 8 sec. / Electron dose: 52.88 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2564
Details: Images were collected as movies with 80 images collected per movie at 100 ms of exposure for a total of 8.0 sec of exposure per micrograph
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5824model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3922227
Details: Particles were picked using Blob Picker in CryoSPARC with min particle diameter 80 A, max particle diameter 120 A, and min separation distance 40 A. 5974094 picks were reduced with an ...Details: Particles were picked using Blob Picker in CryoSPARC with min particle diameter 80 A, max particle diameter 120 A, and min separation distance 40 A. 5974094 picks were reduced with an Inspect Picks Job to 4494189, and an Extract Mics. (G) job reduced picks further to 3922227.
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 743562 / Algorithm: BACK PROJECTION
Details: Non-uniform refinement in CryosPARC with D2 symmetry and refinement mask excluding neighboring particles in psuedo-filaments present in micrographs.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: Initial fitting was done in chimeraX, and refined through sequential Real space refinement protocol in PHENIX and manual refinement with ISOLDE
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 40.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00267496
ELECTRON MICROSCOPYf_angle_d0.518510140
ELECTRON MICROSCOPYf_chiral_restr0.04281200
ELECTRON MICROSCOPYf_plane_restr0.00881308
ELECTRON MICROSCOPYf_dihedral_angle_d12.852648
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints3.7286707255957E-11
ens_1d_3CCELECTRON MICROSCOPYNCS constraints5.9526838006476E-11
ens_1d_4CCELECTRON MICROSCOPYNCS constraints7.4895384259233E-12

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