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- PDB-6z1l: A de novo Enzyme for the Morita-Baylis-Hillman Reaction BH32.12 -

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Basic information

Entry
Database: PDB / ID: 6z1l
TitleA de novo Enzyme for the Morita-Baylis-Hillman Reaction BH32.12
ComponentsBH32.12 protein
KeywordsBIOSYNTHETIC PROTEIN / Morita-Baylis-Hillman Reaction / engineered / evolved
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, 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

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Assembly

Deposited unit
A: BH32.12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7173
Polymers27,5601
Non-polymers1572
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-4 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.967, 70.967, 118.768
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

#1: Protein BH32.12 protein


Mass: 27559.633 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
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: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M SPG 9.0 25 % w/v PEG 1500 / Temp details: Cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.29→42.71 Å / Num. obs: 16121 / % possible obs: 99.55 % / Redundancy: 9.8 % / Biso Wilson estimate: 65.33 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0806 / Rpim(I) all: 0.02701 / Rrim(I) all: 0.08509 / Net I/σ(I): 10.51
Reflection shellResolution: 2.29→2.372 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.617 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 1571 / CC1/2: 0.603 / CC star: 0.867 / Rpim(I) all: 0.5474 / % possible all: 98.66

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Processing

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

6q7o


Resolution: 2.29→42.71 Å / SU ML: 0.3306 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.9881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2616 824 5.13 %
Rwork0.2226 15238 -
obs0.2244 16062 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.73 Å2
Refinement stepCycle: LAST / Resolution: 2.29→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 9 43 1868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611885
X-RAY DIFFRACTIONf_angle_d1.07422539
X-RAY DIFFRACTIONf_chiral_restr0.0598274
X-RAY DIFFRACTIONf_plane_restr0.0074324
X-RAY DIFFRACTIONf_dihedral_angle_d25.1874723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.430.37991550.3092444X-RAY DIFFRACTION98.75
2.43-2.620.31211550.2712465X-RAY DIFFRACTION99.51
2.62-2.880.371240.3052535X-RAY DIFFRACTION99.77
2.89-3.30.30141210.27222540X-RAY DIFFRACTION99.85
3.3-4.160.25791580.22662526X-RAY DIFFRACTION99.48
4.16-42.710.2121110.18442728X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -20.9491046743 Å / Origin y: 26.477902989 Å / Origin z: -11.0134784038 Å
111213212223313233
T0.538654723669 Å2-0.0144247830991 Å20.0573999529735 Å2-0.598950817262 Å2-0.0070586163999 Å2--0.529649284205 Å2
L0.368383478013 °20.652800675837 °20.347732121434 °2-3.84023065274 °23.15916181941 °2--3.36285337426 °2
S-0.0398932756753 Å °-0.0684818255978 Å °-0.016055152549 Å °-0.0997149036566 Å °0.169932203412 Å °-0.147596562657 Å °-0.0475523062653 Å °0.158963848116 Å °-0.15217427316 Å °
Refinement TLS groupSelection details: all

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