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- PDB-5xe8: Crystal Structure of the Peptidase Domain of Streptococcus mutans ComA -

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Basic information

Entry
Database: PDB / ID: 5xe8
TitleCrystal Structure of the Peptidase Domain of Streptococcus mutans ComA
ComponentsPutative ABC transporter, ATP-binding protein ComA
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Peptidase / Quorum-sensing / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


single-species submerged biofilm formation / ABC-type bacteriocin transporter activity / ATPase-coupled lipid transmembrane transporter activity / cysteine-type peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / membrane / metal ion binding
Similarity search - Function
Peptidase C39, ABC-type bacteriocin transporter / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Cysteine proteinases / Type 1 protein exporter / Cathepsin B; Chain A / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. ...Peptidase C39, ABC-type bacteriocin transporter / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Cysteine proteinases / Type 1 protein exporter / Cathepsin B; Chain A / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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 / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / ABC transporter, ATP-binding protein ComA
Similarity search - Component
Biological speciesStreptococcus mutans serotype c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsIshii, S. / Fukui, K. / Yokoshima, S. / Kumagai, K. / Beniyama, Y. / Kodama, T. / Fukuyama, T. / Okabe, T. / Nagano, T. / Kojima, H. / Yano, T.
CitationJournal: Sci Rep / Year: 2017
Title: High-throughput Screening of Small Molecule Inhibitors of the Streptococcus Quorum-sensing Signal Pathway
Authors: Ishii, S. / Fukui, K. / Yokoshima, S. / Kumagai, K. / Beniyama, Y. / Kodama, T. / Fukuyama, T. / Okabe, T. / Nagano, T. / Kojima, H. / Yano, T.
History
DepositionApr 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ABC transporter, ATP-binding protein ComA
C: Putative ABC transporter, ATP-binding protein ComA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9204
Polymers34,7082
Non-polymers2122
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-8 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.071, 59.437, 121.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative ABC transporter, ATP-binding protein ComA


Mass: 17353.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first methionine and the last 16 residues are not identified in the crystal structure.
Source: (gene. exp.) Streptococcus mutans serotype c (bacteria)
Strain: ATCC 700610 / UA159 / Gene: SMU_286 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q8DW05
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100mM ammonium sulfate, 50mM bis-tris, 12.5%(W/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 6597 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 29
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.557

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data scaling
PHENIXphasing
REFMACrefinement
PHENIXmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K8U

3k8u


Resolution: 3.1→31.551 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.31
RfactorNum. reflection% reflection
Rfree0.2693 308 4.67 %
Rwork0.2363 --
obs0.2379 6597 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→31.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 14 1 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042095
X-RAY DIFFRACTIONf_angle_d0.962828
X-RAY DIFFRACTIONf_dihedral_angle_d13.7471262
X-RAY DIFFRACTIONf_chiral_restr0.051318
X-RAY DIFFRACTIONf_plane_restr0.005355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1003-3.90490.30751550.25623063X-RAY DIFFRACTION100
3.9049-31.55210.25031530.22723226X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -3.0367 Å / Origin y: 2.5087 Å / Origin z: 42.7215 Å
111213212223313233
T0.185 Å2-0.1147 Å2-0.06 Å2-0.1911 Å2-0.0879 Å2--0.3852 Å2
L4.096 °2-1.5675 °2-0.3251 °2-8.9204 °2-2.3709 °2--6.6512 °2
S-0.1102 Å °-0.3925 Å °0.1469 Å °0.4827 Å °-0.078 Å °-1.0921 Å °-0.144 Å °-0.1554 Å °-0.0316 Å °
Refinement TLS groupSelection details: all

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