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- PDB-6hee: Crystal structure of Extracellular Domain 1 (ECD1) of FtsX from S... -

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Basic information

Entry
Database: PDB / ID: 6hee
TitleCrystal structure of Extracellular Domain 1 (ECD1) of FtsX from S. pneumonie in complex with undecyl-maltoside
ComponentsCell division protein FtsX
KeywordsCELL CYCLE / cell division / MEMBRANE PROTEIN
Function / homology
Function and homology information


cell division / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #3040 / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein FtsX
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsMartinez-Caballero, S. / Alcorlo-Pages, M. / Hermoso, J.A.
CitationJournal: Mbio / Year: 2019
Title: Structure of the Large Extracellular Loop of FtsX and Its Interaction with the Essential Peptidoglycan Hydrolase PcsB in Streptococcus pneumoniae.
Authors: Rued, B.E. / Alcorlo, M. / Edmonds, K.A. / Martinez-Caballero, S. / Straume, D. / Fu, Y. / Bruce, K.E. / Wu, H. / Havarstein, L.S. / Hermoso, J.A. / Winkler, M.E. / Giedroc, D.P.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 protein FtsX
B: Cell division protein FtsX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3665
Polymers26,6512
Non-polymers7153
Water37821
1
A: Cell division protein FtsX
hetero molecules

B: Cell division protein FtsX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3665
Polymers26,6512
Non-polymers7153
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2260 Å2
ΔGint-23 kcal/mol
Surface area14910 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-14 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.610, 84.610, 106.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cell division protein FtsX


Mass: 13325.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Strain: D39 / NCTC 7466 / Gene: ftsX, SPD_0660 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04LE4
#2: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.57 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: ammonium sulfate, sodium and potassium tartrate and sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→42.31 Å / Num. obs: 17731 / % possible obs: 98.89 % / Redundancy: 22.1 % / Rpim(I) all: 0.004 / Net I/σ(I): 44.14
Reflection shellResolution: 2.3→2.38 Å / Rpim(I) all: 0.092

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementStarting model: 6HE6

6he6


Resolution: 2.3→42.31 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.18
RfactorNum. reflection% reflection
Rfree0.2976 922 5.2 %
Rwork0.2607 --
obs0.2626 17717 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 47 21 1800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081799
X-RAY DIFFRACTIONf_angle_d0.9872429
X-RAY DIFFRACTIONf_dihedral_angle_d5.1641086
X-RAY DIFFRACTIONf_chiral_restr0.062278
X-RAY DIFFRACTIONf_plane_restr0.006310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.42130.40911360.32132332X-RAY DIFFRACTION100
2.4213-2.5730.30521370.30612333X-RAY DIFFRACTION100
2.573-2.77170.38761360.29822348X-RAY DIFFRACTION100
2.7717-3.05050.36081330.30342370X-RAY DIFFRACTION100
3.0505-3.49180.33651170.28642408X-RAY DIFFRACTION100
3.4918-4.39870.28781230.2342432X-RAY DIFFRACTION100
4.3987-44.98160.2531400.24542572X-RAY DIFFRACTION100

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