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- PDB-5oon: Structure of Undecaprenyl-Pyrophosphate Phosphatase, BacA -

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Basic information

Entry
Database: PDB / ID: 5oon
TitleStructure of Undecaprenyl-Pyrophosphate Phosphatase, BacA
ComponentsUndecaprenyl-diphosphatase
KeywordsMEMBRANE PROTEIN / Antibiotic / bacterial cell wall / enzyme mechanism / Escherichia coli / in meso in situ serial crystallography / IMISX / interdigitated inverted topology repeat / lipid cubic phase / peptidoglycan / phosphatase / pyrophosphorylase / undecaprenyl-pyrophosphate
Function / homology
Function and homology information


undecaprenyl-diphosphate phosphatase / undecaprenyl-diphosphatase activity / peptidoglycan biosynthetic process / dephosphorylation / cell wall organization / regulation of cell shape / membrane => GO:0016020 / response to antibiotic / plasma membrane
Similarity search - Function
Undecaprenyl-diphosphatase UppP / Bacitracin resistance protein BacA
Similarity search - Domain/homology
: / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Undecaprenyl-diphosphatase / Undecaprenyl-diphosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsHuang, C.-Y. / Olieric, V. / Warshamanage, R. / Wang, M. / Howe, N. / Ghachi, M.E.I. / Weichert, D. / Kerff, F. / Stansfeld, P. / Touze, T. / Caffrey, M.
Funding support Ireland, Germany, France, 3items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1255 Ireland
German Research Foundation Germany
Biotechnology and Biological Sciences Research CouncilBB/I019855/1 France
CitationJournal: Nat Commun / Year: 2018
Title: Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis.
Authors: El Ghachi, M. / Howe, N. / Huang, C.Y. / Olieric, V. / Warshamanage, R. / Touze, T. / Weichert, D. / Stansfeld, P.J. / Wang, M. / Kerff, F. / Caffrey, M.
History
DepositionAug 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 6, 2018Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Undecaprenyl-diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1246
Polymers30,8881
Non-polymers1,2365
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-32 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.260, 145.000, 40.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Undecaprenyl-diphosphatase / Bacitracin resistance protein / Undecaprenyl pyrophosphate phosphatase


Mass: 30887.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bacA, uppP / Production host: Escherichia coli DH1 (bacteria)
References: UniProt: C3SU37, UniProt: P60933*PLUS, undecaprenyl-diphosphate phosphatase
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 40 % PEG-400, 0.3-0.5 M ammonium citrate dibasic and 0.1 M sodium citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.6→44.84 Å / Num. obs: 19853 / % possible obs: 100 % / Redundancy: 17.91 % / CC1/2: 0.99 / Rrim(I) all: 0.4 / Net I/σ(I): 8.75
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 12.33 % / Mean I/σ(I) obs: 1.87 / CC1/2: 0.25 / Rrim(I) all: 2.03 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12rc2_2821: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.6→44.455 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 990 4.99 %
Rwork0.2058 --
obs0.2077 19853 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→44.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 57 6 2119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062166
X-RAY DIFFRACTIONf_angle_d0.8652929
X-RAY DIFFRACTIONf_dihedral_angle_d11.6261251
X-RAY DIFFRACTIONf_chiral_restr0.047344
X-RAY DIFFRACTIONf_plane_restr0.005356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5999-2.73690.33971430.27492716X-RAY DIFFRACTION100
2.7369-2.90840.31631400.25762698X-RAY DIFFRACTION100
2.9084-3.13290.2731420.22862685X-RAY DIFFRACTION100
3.1329-3.44810.26351400.21542689X-RAY DIFFRACTION100
3.4481-3.94670.22591430.1962682X-RAY DIFFRACTION100
3.9467-4.97140.24591400.18232696X-RAY DIFFRACTION100
4.9714-44.46110.19441420.18882697X-RAY DIFFRACTION100

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