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- PDB-6z4w: FtsE structure from Streptococcus pneumoniae in complex with ADP ... -

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Basic information

Entry
Database: PDB / ID: 6z4w
TitleFtsE structure from Streptococcus pneumoniae in complex with ADP (space group P 1)
ComponentsCell division ATP-binding protein FtsE
KeywordsCELL CYCLE / Cell division / divisome / FtsEX / ATP-binding protein
Function / homology
Function and homology information


transmembrane transporter activity / transmembrane transport / cell cycle / cell division / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Cell division protein FtsE, ATP-binding / ABC transporter, lipoprotein release, LolD / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cell division ATP-binding protein FtsE / Cell division ATP-binding protein FtsE
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.36 Å
AuthorsAlcorlo, M. / Straume, D. / Hermoso, J.A. / Havarstein, L.S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-90030-P Spain
CitationJournal: Mbio / Year: 2020
Title: Structural Characterization of the Essential Cell Division Protein FtsE and Its Interaction with FtsX in Streptococcus pneumoniae.
Authors: Alcorlo, M. / Straume, D. / Lutkenhaus, J. / Havarstein, L.S. / Hermoso, J.A.
History
DepositionMay 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 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

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Assembly

Deposited unit
A: Cell division ATP-binding protein FtsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2622
Polymers25,8351
Non-polymers4271
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-5 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.387, 36.711, 41.106
Angle α, β, γ (deg.)105.270, 95.690, 99.690
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cell division ATP-binding protein FtsE


Mass: 25834.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ftsE_1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A064BZ20, UniProt: Q8DQH4*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.83 Å3/Da / Density % sol: 32.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.15 M NaF and 16% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.36→39.201 Å / Num. obs: 37746 / % possible obs: 95.8 % / Redundancy: 8.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.5
Reflection shellResolution: 1.36→1.38 Å / Rmerge(I) obs: 0.932 / Num. unique obs: 1797 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.36→39.201 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1945 1916 5.08 %
Rwork0.1764 35822 -
obs0.1774 37738 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.97 Å2 / Biso mean: 17.6443 Å2 / Biso min: 6.64 Å2
Refinement stepCycle: final / Resolution: 1.36→39.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 39 298 2151
Biso mean--12.98 25.79 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.36-1.3940.31781370.2649244692
1.394-1.43170.29611500.2477250094
1.4317-1.47380.28661100.2375253494
1.4738-1.52140.24661270.2214253494
1.5214-1.57580.22891290.2062254295
1.5758-1.63890.23271330.1886251595
1.6389-1.71350.22191320.1811255395
1.7135-1.80380.2121190.1857256996
1.8038-1.91680.2051480.1786260097
1.9168-2.06480.20641270.1701260697
2.0648-2.27260.20371340.1693259797
2.2726-2.60140.19471470.1808259198
2.6014-3.27720.17841460.1692261498
3.2772-39.2010.15741770.1491262199

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