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- PDB-3k8u: Crystal Structure of the Peptidase Domain of Streptococcus ComA, ... -

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Basic information

Entry
Database: PDB / ID: 3k8u
TitleCrystal Structure of the Peptidase Domain of Streptococcus ComA, a Bi-functional ABC Transporter Involved in Quorum Sensing Pathway
ComponentsPutative ABC transporter, ATP-binding protein ComA
KeywordsHYDROLASE / ABC Transporter / ComA / Cysteine Protease / Quorum-sensing / Streptococcus
Function / homology
Function and homology information


single-species submerged biofilm formation / ABC-type bacteriocin 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
ABC transporter, ATP-binding protein ComA
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsIshii, S. / Yano, T. / Ebihara, A. / Okamoto, A. / Manzoku, M. / Hayashi, H.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of the peptidase domain of Streptococcus ComA, a bifunctional ATP-binding cassette transporter involved in the quorum-sensing pathway
Authors: Ishii, S. / Yano, T. / Ebihara, A. / Okamoto, A. / Manzoku, M. / Hayashi, H.
History
DepositionOct 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)17,9931
Polymers17,9931
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.610, 58.610, 112.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

21A-240-

HOH

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Components

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


Mass: 17992.570 Da / Num. of mol.: 1 / Fragment: peptidase domain, residues 45-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8DW05
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 16% polyethylene glycol 3350, 0.16M di-ammonium hydrogen citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B210.9789, 0.9000, 0.9795
SYNCHROTRONSPring-8 BL26B221
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDOct 6, 2007
MARMOSAIC 225 mm CCD2CCDNov 27, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI Double-CrystalMADMx-ray1
2SI Double-CrystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.91
30.97951
411
ReflectionResolution: 1.9→50 Å / Num. obs: 16136 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 45
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 10.2 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→41.44 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1517854.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1614 10.1 %RANDOM
Rwork0.212 ---
obs0.212 16053 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.2418 Å2 / ksol: 0.370146 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å20 Å20 Å2
2--2.39 Å20 Å2
3----4.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 0 95 1186
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.671.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.562.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 259 10 %
Rwork0.23 2340 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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