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- PDB-7o1d: A de novo Enzyme for the Morita-Baylis-Hillman Reaction BH32.7 -

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Basic information

Entry
Database: PDB / ID: 7o1d
TitleA de novo Enzyme for the Morita-Baylis-Hillman Reaction BH32.7
ComponentsBH32.7 protein
KeywordsBIOSYNTHETIC PROTEIN / de novo enzyme
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC)757991 United Kingdom
CitationJournal: Nat.Chem. / Year: 2022
Title: Engineering an efficient and enantioselective enzyme for the Morita-Baylis-Hillman reaction.
Authors: Crawshaw, R. / Crossley, A.E. / Johannissen, L. / Burke, A.J. / Hay, S. / Levy, C. / Baker, D. / Lovelock, S.L. / Green, A.P.
History
DepositionMar 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BH32.7 protein


Theoretical massNumber of molelcules
Total (without water)27,5321
Polymers27,5321
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.560, 69.630, 45.720
Angle α, β, γ (deg.)90.000, 99.290, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein BH32.7 protein


Mass: 27531.641 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bicine pH 9.3 25% PEG smear medium BCS screen condition B6
Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→45.12 Å / Num. obs: 20803 / % possible obs: 99 % / Redundancy: 3.1 % / Biso Wilson estimate: 34.48 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.0366 / Rpim(I) all: 0.0246 / Rrim(I) all: 0.044 / Net I/σ(I): 17.7
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 4.27 / Num. unique obs: 6531 / CC1/2: 0.919 / CC star: 0.979 / Rpim(I) all: 0.167 / % possible all: 98.55

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Inhouse

Resolution: 1.8→45.12 Å / SU ML: 0.2514 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2546 1067 5.13 %
Rwork0.2039 19736 -
obs0.2064 20803 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.94 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 0 148 1969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00391866
X-RAY DIFFRACTIONf_angle_d0.53832513
X-RAY DIFFRACTIONf_chiral_restr0.0429275
X-RAY DIFFRACTIONf_plane_restr0.0044321
X-RAY DIFFRACTIONf_dihedral_angle_d14.1248714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.35621410.29892417X-RAY DIFFRACTION98.8
1.88-1.980.30631300.252475X-RAY DIFFRACTION99.43
1.98-2.110.27511230.24422469X-RAY DIFFRACTION99.39
2.11-2.270.25791370.21732465X-RAY DIFFRACTION99.35
2.27-2.50.2861390.21272473X-RAY DIFFRACTION99.54
2.5-2.860.29231330.23132484X-RAY DIFFRACTION99.13
2.86-3.60.26371400.20552471X-RAY DIFFRACTION99.01
3.6-45.120.21141240.17472482X-RAY DIFFRACTION97.42
Refinement TLS params.Method: refined / Origin x: -14.1967858522 Å / Origin y: -12.2305804039 Å / Origin z: -11.2380455318 Å
111213212223313233
T0.249617664716 Å20.0326763955229 Å20.00642837538409 Å2-0.214198186994 Å20.0417435754836 Å2--0.250852591618 Å2
L1.25764676775 °20.819662380233 °20.379905633988 °2-1.3828019914 °20.607651899124 °2--1.34735829696 °2
S0.0234733161521 Å °-0.100732921659 Å °-0.061186384868 Å °0.145432091702 Å °-0.0988063925536 Å °-0.0113972876784 Å °0.152948188964 Å °0.0404584375046 Å °0.000283595521279 Å °
Refinement TLS groupSelection details: all

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