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- PDB-8p4w: Lactobacillus plantarum LpdD mutant - H35A -

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Basic information

Entry
Database: PDB / ID: 8p4w
TitleLactobacillus plantarum LpdD mutant - H35A
ComponentsProtein LpdD
KeywordsFLAVOPROTEIN / UbiD / UbiX / LpdD
Function / homology: / Prenylated flavin chaperone LpdD-like domain / PHOSPHATE ION / Protein LpdD
Function and homology information
Biological speciesLactiplantibacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.78 Å
AuthorsGahloth, D. / Leys, D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The prFMNH 2 -binding chaperone LpdD assists UbiD decarboxylase activation.
Authors: Gahloth, D. / Fisher, K. / Marshall, S. / Leys, D.
History
DepositionMay 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Assembly

Deposited unit
A: Protein LpdD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1412
Polymers15,0461
Non-polymers951
Water2,666148
1
A: Protein LpdD
hetero molecules

A: Protein LpdD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2824
Polymers30,0922
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2210 Å2
ΔGint-30 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.970, 58.970, 83.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21A-438-

HOH

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Components

#1: Protein Protein LpdD / Gallate decarboxylase subunit D


Mass: 15045.983 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum (bacteria)
Gene: lpdD, lp_0272
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: F9UT68
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M Sodium Acetate pH 4.6, 2.0M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.73→48.146 Å / Num. obs: 15850 / % possible obs: 100 % / Redundancy: 17 % / CC1/2: 1 / Net I/σ(I): 13.4
Reflection shellResolution: 1.73→1.76 Å / Num. unique obs: 748 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.78→48.146 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 663 4.54 %
Rwork0.194 --
obs0.1951 14618 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→48.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 5 148 1068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006936
X-RAY DIFFRACTIONf_angle_d0.7491274
X-RAY DIFFRACTIONf_dihedral_angle_d2.564558
X-RAY DIFFRACTIONf_chiral_restr0.052152
X-RAY DIFFRACTIONf_plane_restr0.006162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.91740.32731290.282670X-RAY DIFFRACTION98
1.9174-2.11040.23181410.21982748X-RAY DIFFRACTION100
2.1104-2.41580.221150.19642780X-RAY DIFFRACTION100
2.4158-3.04360.22821380.20032793X-RAY DIFFRACTION100
3.0436-48.1460.20191400.17592964X-RAY DIFFRACTION100

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