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- PDB-2pfy: Crystal structure of DctP7, a Bordetella pertussis extracytoplasm... -

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Basic information

Entry
Database: PDB / ID: 2pfy
TitleCrystal structure of DctP7, 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 / SAD / Resolution: 1.95 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Putative exported protein
B: Putative exported protein
C: Putative exported protein
D: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7638
Polymers132,2464
Non-polymers5164
Water13,349741
1
A: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1912
Polymers33,0621
Non-polymers1291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1912
Polymers33,0621
Non-polymers1291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1912
Polymers33,0621
Non-polymers1291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1912
Polymers33,0621
Non-polymers1291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.840, 149.750, 169.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative exported protein


Mass: 33061.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Species: Bordetella pertussis / Strain: Tohama I / Gene: BP1891 / Plasmid: pQE30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q7VXB1
#2: Chemical
ChemComp-PCA / PYROGLUTAMIC ACID


Type: L-peptide linking / Mass: 129.114 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H7NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 3.8M Potassium Acetate, 0.1M Sodium Citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.95→112.51 Å / Num. obs: 111077
Reflection shellResolution: 1.95→2 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
DNAdata collection
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→112.51 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.172 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 5579 5 %RANDOM
Rwork0.168 ---
obs0.169 111007 91.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.864 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.95→112.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9232 0 36 754 10022
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.016
X-RAY DIFFRACTIONr_bond_other_d0.003
X-RAY DIFFRACTIONr_angle_refined_deg1.465
X-RAY DIFFRACTIONr_angle_other_deg0.59
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.023
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4
X-RAY DIFFRACTIONr_chiral_restr0.104
X-RAY DIFFRACTIONr_gen_planes_refined0.005
X-RAY DIFFRACTIONr_nbd_refined0.224
X-RAY DIFFRACTIONr_nbd_other0.198
X-RAY DIFFRACTIONr_nbtor_refined0.3
X-RAY DIFFRACTIONr_nbtor_other0.278
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.206
X-RAY DIFFRACTIONr_symmetry_vdw_refined
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 411 -
Rwork0.188 8181 -
obs-8592 97.03 %

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