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- PDB-2f5x: Structure of periplasmic binding protein BugD -

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Basic information

Entry
Database: PDB / ID: 2f5x
TitleStructure of periplasmic binding protein BugD
ComponentsBugD
KeywordsTRANSPORT PROTEIN / periplasmic binding protein
Function / homology
Function and homology information


Bordetella uptake gene, domain 1 / Bordetella uptake gene / Bordetella uptake gene, domain 1 / Tripartite tricarboxylate transporter family receptor / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / : / Exported protein
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsHuvent, I. / Belrhali, H. / Antoine, R. / Bompard, C. / Jacob-Dubuisson, F. / Villeret, V.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Bordetella pertussis BugD Solute Receptor Unveils the Basis of Ligand Binding in a New Family of Periplasmic Binding Proteins
Authors: Huvent, I. / Belrhali, H. / Antoine, R. / Bompard, C. / Locht, C. / Jacob-Dubuisson, F. / Villeret, V.
History
DepositionNov 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 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: BugD
B: BugD
C: BugD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4906
Polymers102,0913
Non-polymers3993
Water19,9431107
1
A: BugD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1632
Polymers34,0301
Non-polymers1331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BugD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1632
Polymers34,0301
Non-polymers1331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BugD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1632
Polymers34,0301
Non-polymers1331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.670, 76.420, 260.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is one monomer. THe asymmetric unit contains three monomers

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Components

#1: Protein BugD


Mass: 34030.348 Da / Num. of mol.: 3 / Fragment: residues 26-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Species: Bordetella pertussis / Strain: Tohama I / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: GenBank: 33594322, UniProt: Q7VTS1*PLUS
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1107 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris 10 mM, (NH4)2SO4 0.2 M, PEG1500 36% (w/v), glycerol 15%, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9791
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.72→49.63 Å / Num. obs: 101925 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Rsym value: 0.072 / Net I/σ(I): 7.1
Reflection shellResolution: 1.72→1.81 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 3 / Rsym value: 0.243 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT1.701data extraction
DENZOdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.72→49.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.382 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.175 5101 5 %RANDOM
Rwork0.14 ---
obs0.14 101925 99.7 %-
all-102090 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.72→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6750 0 27 1107 7884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226921
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.989408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3385895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.21072
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025192
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.23557
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2809
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.263
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7611.54493
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37927247
X-RAY DIFFRACTIONr_scbond_it2.63732428
X-RAY DIFFRACTIONr_scangle_it4.2544.52161
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.76 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.206 382
Rwork0.158 7081
Refinement TLS params.Method: refined / Origin x: 15.133 Å / Origin y: 36.774 Å / Origin z: 1.436 Å
111213212223313233
T0.0158 Å20.0002 Å2-0.0005 Å2-0.0161 Å2-0.002 Å2--0.0002 Å2
L-0.0154 °2-0.0022 °2-0.0002 °2-0.0257 °20.0567 °2--0.3602 °2
S-0.0002 Å °0.0036 Å °-0.0006 Å °-0.0007 Å °-0.0071 Å °0.0061 Å °-0.0181 Å °-0.0095 Å °0.0073 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 30014 - 312
2X-RAY DIFFRACTION1BB1 - 30013 - 312
3X-RAY DIFFRACTION1CC2 - 30014 - 312
4X-RAY DIFFRACTION1AD9011
5X-RAY DIFFRACTION1BE9021
6X-RAY DIFFRACTION1CF9031

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