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- PDB-9aua: PLP-dependent BesB holoenzyme -

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Basic information

Entry
Database: PDB / ID: 9aua
TitlePLP-dependent BesB holoenzyme
ComponentsBesB
KeywordsBIOSYNTHETIC PROTEIN / pyridoxal 5'-phosphate / alkyne
Function / homologyACETATE ION / Chem-AN7
Function and homology information
Biological speciesStreptomyces achromogenes subsp. achromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 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

Downloads & links

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Assembly

Deposited unit
A: BesB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0949
Polymers57,3831
Non-polymers7118
Water9,080504
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)58.640, 58.640, 249.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BesB


Mass: 57382.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces achromogenes subsp. achromogenes (bacteria)
Production host: Rhodococcus jostii RHA1 (bacteria)

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Non-polymers , 5 types, 512 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-AN7 / (3E)-4-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}-2-oxobut-3-enoic acid


Mass: 317.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12NO8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.13 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: 1.29→50.78 Å / Num. obs: 126887 / % possible obs: 99.9 % / Redundancy: 17 % / CC1/2: 0.999 / Rpim(I) all: 0.037 / Net I/σ(I): 12.1
Reflection shellResolution: 1.29→1.31 Å / Redundancy: 17.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6174 / CC1/2: 0.375 / Rpim(I) all: 0.712 / % 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: 1.29→47.0759 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1837 6085 4.8 %
Rwork0.1673 --
obs0.1681 126755 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.29→47.0759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 46 504 4216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053860
X-RAY DIFFRACTIONf_angle_d0.8385278
X-RAY DIFFRACTIONf_dihedral_angle_d11.1292142
X-RAY DIFFRACTIONf_chiral_restr0.076604
X-RAY DIFFRACTIONf_plane_restr0.006700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.30470.34982070.34124027X-RAY DIFFRACTION100
1.3047-1.320.31821950.31753912X-RAY DIFFRACTION100
1.32-1.33610.3132280.314002X-RAY DIFFRACTION100
1.3361-1.3530.31522030.31023884X-RAY DIFFRACTION100
1.353-1.37080.29312250.29523956X-RAY DIFFRACTION100
1.3708-1.38960.291850.27593982X-RAY DIFFRACTION100
1.3896-1.40950.25342360.25283928X-RAY DIFFRACTION100
1.4095-1.43050.2492010.2444011X-RAY DIFFRACTION100
1.4305-1.45290.23732050.23323966X-RAY DIFFRACTION100
1.4529-1.47670.24222110.22073968X-RAY DIFFRACTION100
1.4767-1.50210.22712200.2113971X-RAY DIFFRACTION100
1.5021-1.52950.23051820.19683952X-RAY DIFFRACTION100
1.5295-1.55890.21042100.19674000X-RAY DIFFRACTION100
1.5589-1.59070.2231980.19843998X-RAY DIFFRACTION100
1.5907-1.62530.20661870.18653997X-RAY DIFFRACTION100
1.6253-1.66310.19111650.17544012X-RAY DIFFRACTION100
1.6631-1.70470.17222160.16384017X-RAY DIFFRACTION100
1.7047-1.75080.19942060.15993976X-RAY DIFFRACTION100
1.7508-1.80230.19522320.16163952X-RAY DIFFRACTION100
1.8023-1.86050.17431910.15194037X-RAY DIFFRACTION100
1.8605-1.9270.15471840.15164023X-RAY DIFFRACTION100
1.927-2.00410.16981840.15614056X-RAY DIFFRACTION100
2.0041-2.09530.14982340.14674043X-RAY DIFFRACTION100
2.0953-2.20580.16522290.14173991X-RAY DIFFRACTION100
2.2058-2.3440.16312050.14614076X-RAY DIFFRACTION100
2.344-2.5250.19011830.15494066X-RAY DIFFRACTION100
2.525-2.77910.18081730.15574146X-RAY DIFFRACTION100
2.7791-3.18110.14762120.15244108X-RAY DIFFRACTION100
3.1811-4.00750.15631770.13874197X-RAY DIFFRACTION100
4.0075-47.07590.17432010.16294416X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -23.2061 Å / Origin y: 15.0232 Å / Origin z: 19.0112 Å
111213212223313233
T0.1281 Å20.0034 Å2-0.0069 Å2-0.0913 Å20.0137 Å2--0.1195 Å2
L0.3505 °20.1511 °2-0.0276 °2-0.7385 °2-0.3551 °2--1.0814 °2
S0.0508 Å °-0.0413 Å °0.0212 Å °0.0796 Å °0.0252 Å °0.0777 Å °-0.1032 Å °-0.0773 Å °-0.0463 Å °
Refinement TLS groupSelection details: all

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