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- PDB-6fmw: IMISX-EP of Hg-BacA cocrystallization -

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Basic information

Entry
Database: PDB / ID: 6fmw
TitleIMISX-EP of Hg-BacA cocrystallization
ComponentsUndecaprenyl-diphosphatase
KeywordsHYDROLASE / Serial crystallography / experimental phasing / in meso crystallization / in situ diffraction data collection / membrane protein structure.
Function / homology
Function and homology information


undecaprenyl-diphosphate phosphatase / undecaprenyl-diphosphatase activity / pyrophosphatase activity / peptidoglycan metabolic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsHuang, C.-Y. / Olieric, V. / Howe, N. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Vogeley, L. / Basu, S. / Diederichs, K. / Caffrey, M. / Wang, M.
Funding support Ireland, Switzerland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 Ireland
European Union701647 Switzerland
CitationJournal: Commun Biol / Year: 2018
Title: In situ serial crystallography for rapid de novo membrane protein structure determination.
Authors: Huang, C.Y. / Olieric, V. / Howe, N. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Vogeley, L. / Basu, S. / Diederichs, K. / Caffrey, M. / Wang, M.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2Mar 22, 2023Group: Database references / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-32 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.060, 145.130, 39.990
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 K-12 (bacteria) / Gene: uppP, bacA, upk, b3057, JW3029 / Production host: Escherichia coli (E. coli)
References: UniProt: P60932, 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
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: Oct 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.6→44.536 Å / Num. obs: 19671 / % possible obs: 99 % / Redundancy: 20.7 % / Rrim(I) all: 0.38 / Net I/σ(I): 8.95
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 15.7 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 1467 / Rrim(I) all: 2 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.13rc1_2954: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXDEphasing
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→44.536 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.51
RfactorNum. reflection% reflection
Rfree0.2543 975 4.96 %
Rwork0.224 --
obs0.2256 19671 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→44.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 57 6 2119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032166
X-RAY DIFFRACTIONf_angle_d0.642929
X-RAY DIFFRACTIONf_dihedral_angle_d5.4881690
X-RAY DIFFRACTIONf_chiral_restr0.04344
X-RAY DIFFRACTIONf_plane_restr0.003356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.73710.29711350.28142630X-RAY DIFFRACTION98
2.7371-2.90860.36261340.27332675X-RAY DIFFRACTION99
2.9086-3.13310.28121440.25572677X-RAY DIFFRACTION100
3.1331-3.44830.28581430.24392675X-RAY DIFFRACTION100
3.4483-3.9470.25691410.21682683X-RAY DIFFRACTION100
3.947-4.97180.24811360.20012673X-RAY DIFFRACTION100
4.9718-44.54290.19871420.20152683X-RAY DIFFRACTION100

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