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- PDB-6z1k: A de novo Enzyme for the Morita-Baylis-Hillman Reaction BH32.6 -

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Basic information

Entry
Database: PDB / ID: 6z1k
TitleA de novo Enzyme for the Morita-Baylis-Hillman Reaction BH32.6
ComponentsBH32.6 protein
KeywordsBIOSYNTHETIC PROTEIN / Morita-Baylis-Hillman Reaction / engineered / evolved
Function / homologyFORMIC ACID / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)757991 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M027023/1 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
DepositionMay 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
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
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 1.3Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: BH32.6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8566
Polymers27,5561
Non-polymers3005
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-8 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.690, 71.690, 121.272
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BH32.6 protein


Mass: 27555.598 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)

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Non-polymers , 5 types, 247 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.26 Å3/Da / Density % sol: 62.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol 0.03 M of each divalent cation 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.48→55.26 Å / Num. obs: 60772 / % possible obs: 99.9 % / Redundancy: 9.5 % / Biso Wilson estimate: 26.4 Å2 / CC1/2: 0.997 / CC star: 0.99 / Rmerge(I) obs: 0.05985 / Rpim(I) all: 0.02062 / Rrim(I) all: 0.0634 / Net I/σ(I): 14.64
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.411 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 5941 / CC1/2: 0.679 / CC star: 0.899 / Rpim(I) all: 0.477 / % possible all: 99.13

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
PHENIX1.18.1_3865refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q7O

6q7o


Resolution: 1.48→55.26 Å / SU ML: 0.1471 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.4185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1771 3038 5 %
Rwork0.1572 57723 -
obs0.1582 60761 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.89 Å2
Refinement stepCycle: LAST / Resolution: 1.48→55.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 18 242 2105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872013
X-RAY DIFFRACTIONf_angle_d1.13322718
X-RAY DIFFRACTIONf_chiral_restr0.0768291
X-RAY DIFFRACTIONf_plane_restr0.0076354
X-RAY DIFFRACTIONf_dihedral_angle_d19.8064784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.27271490.24232544X-RAY DIFFRACTION98.11
1.5-1.530.26081340.2162583X-RAY DIFFRACTION100
1.53-1.550.25541450.20832573X-RAY DIFFRACTION99.93
1.55-1.580.24331310.19072587X-RAY DIFFRACTION99.96
1.58-1.610.26731480.19722580X-RAY DIFFRACTION99.93
1.61-1.650.21481640.17462562X-RAY DIFFRACTION99.96
1.65-1.680.18131460.162611X-RAY DIFFRACTION99.96
1.68-1.720.17981220.14552612X-RAY DIFFRACTION100
1.72-1.760.1571280.14722597X-RAY DIFFRACTION99.96
1.76-1.810.20081220.13142602X-RAY DIFFRACTION100
1.81-1.860.16181530.13842591X-RAY DIFFRACTION100
1.86-1.920.15831400.12612616X-RAY DIFFRACTION99.96
1.92-1.990.1711260.14512653X-RAY DIFFRACTION100
1.99-2.070.18731270.14062609X-RAY DIFFRACTION100
2.07-2.170.18751380.14832637X-RAY DIFFRACTION100
2.17-2.280.18761190.13542624X-RAY DIFFRACTION100
2.28-2.420.1711530.14972624X-RAY DIFFRACTION100
2.43-2.610.181590.14912622X-RAY DIFFRACTION100
2.61-2.870.15761280.16992675X-RAY DIFFRACTION100
2.88-3.290.2001960.16082705X-RAY DIFFRACTION100
3.29-4.140.14951510.15652697X-RAY DIFFRACTION100
4.15-55.260.18161590.16562819X-RAY DIFFRACTION99.93

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