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- PDB-9aub: PLP-dependent BesB-F231Y variant holoenzyme -

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Basic information

Entry
Database: PDB / ID: 9aub
TitlePLP-dependent BesB-F231Y variant holoenzyme
ComponentsBesB F231Y variant
KeywordsBIOSYNTHETIC PROTEIN / pyridoxal 5'-phosphate / alkyne
Biological speciesStreptomyces achromogenes subsp. achromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsHedges, J.B. / Ryan, K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Terminal alkyne formation by a pyridoxal phosphate-dependent enzyme.
Authors: Hedges, J.B. / Marchand, J.A. / Calvo-Tusell, C. / Wei, Z.W. / Millar, D.C. / Garcia-Borras, M. / Chang, M.C.Y. / Ryan, K.S.
History
DepositionFeb 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BesB F231Y variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0227
Polymers57,6271
Non-polymers3956
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.520, 58.520, 250.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

#1: Protein BesB F231Y variant


Mass: 57626.992 Da / Num. of mol.: 1 / Mutation: F231Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces achromogenes subsp. achromogenes (bacteria)
Production host: Rhodococcus jostii RHA1 (bacteria)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.16 M magnesium acetate, 0.08 M Tris, 14-22% PEG 8000, and 15-20% glycerol, 4-10 mg/mL SAcBesB

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.49→46.97 Å / Num. obs: 82643 / % possible obs: 99.8 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rpim(I) all: 0.046 / Net I/σ(I): 11.8
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4034 / CC1/2: 0.35 / Rpim(I) all: 0.957 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→46.97 Å / SU ML: 0.1693 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4039 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1912 4124 5 %
Rwork0.167 78388 -
obs0.1683 82512 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.05 Å2
Refinement stepCycle: LAST / Resolution: 1.49→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 25 461 4159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053781
X-RAY DIFFRACTIONf_angle_d0.82695158
X-RAY DIFFRACTIONf_chiral_restr0.0767592
X-RAY DIFFRACTIONf_plane_restr0.0061676
X-RAY DIFFRACTIONf_dihedral_angle_d15.59722110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.31841410.3172669X-RAY DIFFRACTION100
1.51-1.530.32911750.30932585X-RAY DIFFRACTION99.82
1.53-1.550.30571220.31292698X-RAY DIFFRACTION99.79
1.55-1.570.30881270.28992666X-RAY DIFFRACTION99.89
1.57-1.590.30061220.28492733X-RAY DIFFRACTION99.55
1.59-1.610.30391140.25972639X-RAY DIFFRACTION99.93
1.61-1.630.26531260.23022718X-RAY DIFFRACTION99.89
1.63-1.660.30041180.22642665X-RAY DIFFRACTION99.96
1.66-1.690.23491460.21452685X-RAY DIFFRACTION99.89
1.69-1.720.25181450.20192677X-RAY DIFFRACTION99.79
1.72-1.750.23961510.20122632X-RAY DIFFRACTION99.86
1.75-1.780.21711540.18972681X-RAY DIFFRACTION99.82
1.78-1.820.20751240.19052685X-RAY DIFFRACTION99.79
1.82-1.860.23661390.18182621X-RAY DIFFRACTION99.71
1.86-1.90.19621130.17722742X-RAY DIFFRACTION99.65
1.9-1.950.20311310.16672735X-RAY DIFFRACTION99.65
1.95-20.21611180.1542673X-RAY DIFFRACTION99.96
2-2.060.17151270.15212713X-RAY DIFFRACTION99.93
2.06-2.120.15461440.14872705X-RAY DIFFRACTION99.93
2.12-2.20.17921650.14572691X-RAY DIFFRACTION99.96
2.2-2.290.17861620.14912664X-RAY DIFFRACTION100
2.29-2.390.18721530.15362678X-RAY DIFFRACTION99.02
2.39-2.520.17811500.15642731X-RAY DIFFRACTION99.93
2.52-2.680.18811560.16072746X-RAY DIFFRACTION100
2.68-2.880.19241520.15692724X-RAY DIFFRACTION100
2.88-3.170.2031250.15292777X-RAY DIFFRACTION100
3.17-3.630.17121940.14432718X-RAY DIFFRACTION98.71
3.63-4.580.15021640.13152798X-RAY DIFFRACTION99.97
4.58-46.970.17991660.17352939X-RAY DIFFRACTION98.6
Refinement TLS params.Method: refined / Origin x: -33.7049027239 Å / Origin y: 12.5201372712 Å / Origin z: -22.5507312002 Å
111213212223313233
T0.122044021177 Å20.0123966824612 Å20.0172305048206 Å2-0.136720224572 Å20.000161531521399 Å2--0.150070360992 Å2
L0.633882857722 °2-0.232914857062 °2-0.305698800751 °2-0.662276125882 °20.20215293844 °2--1.16165830837 °2
S0.0365963321586 Å °-0.0563638521199 Å °0.0608443708229 Å °0.0728309965308 Å °0.0549921022333 Å °-0.0526286848123 Å °-0.0256253687731 Å °0.105865766553 Å °-0.0715439222965 Å °
Refinement TLS groupSelection details: all

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