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- PDB-2pfz: Crystal structure of DctP6, a Bordetella pertussis extracytoplasm... -

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Basic information

Entry
Database: PDB / ID: 2pfz
TitleCrystal structure of DctP6, a Bordetella pertussis extracytoplasmic solute receptor binding pyroglutamic acid
ComponentsPutative exported protein
KeywordsTRANSPORT PROTEIN / extracytoplasmic solute receptor / tripartite ATP independent periplasmic transport / pyroglutamic acid / ligand binding
Function / homology
Function and homology information


transmembrane transport
Similarity search - Function
Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYROGLUTAMIC ACID / Exported protein
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRucktooa, P.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of two Bordetella pertussis Periplasmic Receptors Contribute to Defining a Novel Pyroglutamic Acid Binding DctP Subfamily.
Authors: Rucktooa, P. / Antoine, R. / Herrou, J. / Huvent, I. / Locht, C. / Jacob-Dubuisson, F. / Villeret, V. / Bompard, C.
History
DepositionApr 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4792
Polymers33,3501
Non-polymers1291
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.390, 108.390, 63.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-325-

HOH

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Components

#1: Protein Putative exported protein


Mass: 33350.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Species: Bordetella pertussis / Strain: Tohama I / Gene: bp1887 / Plasmid: pQE30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q7VXB3
#2: Chemical ChemComp-PCA / PYROGLUTAMIC ACID


Type: L-peptide linking / Mass: 129.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 36% (w/v) PEG 2000 MME, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97942 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.8→19.85 Å / Num. all: 35380 / Num. obs: 35219

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
DNAdata collection
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.85 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.782 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1765 5 %RANDOM
Rwork0.187 ---
obs0.189 35219 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.257 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 9 181 2539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222408
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9673258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56325.784102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88215429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.974156
X-RAY DIFFRACTIONr_chiral_restr0.1160.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021803
X-RAY DIFFRACTIONr_nbd_refined0.2180.21194
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21655
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.29
X-RAY DIFFRACTIONr_mcbond_it0.991.51553
X-RAY DIFFRACTIONr_mcangle_it1.47622401
X-RAY DIFFRACTIONr_scbond_it2.61831005
X-RAY DIFFRACTIONr_scangle_it3.5174.5857
X-RAY DIFFRACTIONr_rigid_bond_restr1.99932558
X-RAY DIFFRACTIONr_sphericity_free5.2353181
X-RAY DIFFRACTIONr_sphericity_bonded2.48132358
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 133 -
Rwork0.221 2411 -
obs-2544 99.57 %

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