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- PDB-8kdl: Crystal structure of LmbF in complex with PLP -

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Basic information

Entry
Database: PDB / ID: 8kdl
TitleCrystal structure of LmbF in complex with PLP
ComponentsAminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
KeywordsLYASE / lincomycin / PLP / biosynthesis
Function / homology: / biosynthetic process / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / pyridoxal phosphate binding / LmbF
Function and homology information
Biological speciesStreptomyces lincolnensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMori, T. / Lyu, S. / Kadlcik, S. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Chem. / Year: 2025
Title: Molecular basis for the diversification of lincosamide biosynthesis by pyridoxal phosphate-dependent enzymes.
Authors: Mori, T. / Moriwaki, Y. / Sakurada, K. / Lyu, S. / Kadlcik, S. / Janata, J. / Mazumdar, A. / Koberska, M. / Terada, T. / Kamenik, Z. / Abe, I.
History
DepositionAug 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
B: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9314
Polymers96,7472
Non-polymers1842
Water15,169842
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-19 kcal/mol
Surface area28400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.277, 74.017, 74.843
Angle α, β, γ (deg.)90.000, 93.183, 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 Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme / LmbF


Mass: 48373.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lincolnensis (bacteria) / Gene: GJU35_01420 / Production host: Escherichia coli (E. coli) / References: UniProt: A9Y8R7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 842 / 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: 1.92 Å3/Da / Density % sol: 36.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6.5, 27% PEG 4000, 0.8M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→48.63 Å / Num. obs: 80638 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 11.39 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.8
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3 / Num. unique obs: 4199 / CC1/2: 0.841 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.63 Å / SU ML: 0.1305 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.2816
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.204 2011 2.49 %
Rwork0.1648 78595 -
obs0.1658 80606 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6412 0 12 842 7266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00686674
X-RAY DIFFRACTIONf_angle_d0.97899131
X-RAY DIFFRACTIONf_chiral_restr0.0596967
X-RAY DIFFRACTIONf_plane_restr0.01141212
X-RAY DIFFRACTIONf_dihedral_angle_d7.5778958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.23371490.19645528X-RAY DIFFRACTION98.95
1.74-1.790.21361390.18155596X-RAY DIFFRACTION99.97
1.79-1.840.2151400.17435583X-RAY DIFFRACTION99.98
1.84-1.90.18841500.16775578X-RAY DIFFRACTION100
1.9-1.970.21071320.16325629X-RAY DIFFRACTION100
1.97-2.050.18071420.1575586X-RAY DIFFRACTION100
2.05-2.140.20011400.1625595X-RAY DIFFRACTION100
2.14-2.250.21091370.16285615X-RAY DIFFRACTION100
2.25-2.40.20791420.16515640X-RAY DIFFRACTION99.98
2.4-2.580.19661480.17155618X-RAY DIFFRACTION100
2.58-2.840.21811470.17445595X-RAY DIFFRACTION99.97
2.84-3.250.22991450.17025631X-RAY DIFFRACTION99.97
3.25-4.10.18841480.15095656X-RAY DIFFRACTION99.98
4.1-48.630.18951520.15615745X-RAY DIFFRACTION99.9

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