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- PDB-2qpq: Structure of Bug27 from Bordetella pertussis -

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Basic information

Entry
Database: PDB / ID: 2qpq
TitleStructure of Bug27 from Bordetella pertussis
Componentsprotein Bug27
KeywordsTRANSPORT PROTEIN / ALPHA/BETA DOMAIN / VENUS FLYTRAP
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Exported protein
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å
AuthorsHerrou, J. / Bompard, C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure-based mechanism of ligand binding for periplasmic solute-binding protein of the Bug family.
Authors: Herrou, J. / Bompard, C. / Antoine, R. / Leroy, A. / Rucktooa, P. / Hot, D. / Huvent, I. / Locht, C. / Villeret, V. / Jacob-Dubuisson, F.
History
DepositionJul 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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_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

Downloads & links

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Assembly

Deposited unit
A: protein Bug27
B: protein Bug27
C: protein Bug27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5695
Polymers95,1853
Non-polymers3842
Water10,989610
1
A: protein Bug27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9202
Polymers31,7281
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: protein Bug27


Theoretical massNumber of molelcules
Total (without water)31,7281
Polymers31,7281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: protein Bug27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9202
Polymers31,7281
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.390, 82.310, 87.470
Angle α, β, γ (deg.)90.00, 95.35, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer

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Components

#1: Protein protein Bug27 / Putative exported protein


Mass: 31728.287 Da / Num. of mol.: 3 / Fragment: residues 30-330 (no signal peptide)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: 2667749 / Plasmid: pQE-30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7W019
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M Na-citrate, 25% (w/v) PEG 2000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-210.933
SYNCHROTRONESRF ID23-120.979, 0.970, 0.979
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
20.9791
30.971
ReflectionResolution: 1.9→6.56 Å / Num. obs: 78417 / % possible obs: 97.3 % / Redundancy: 3.89 % / Rsym value: 0.057 / Net I/σ(I): 0.1484
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.87 % / Mean I/σ(I) obs: 4.64 / Rsym value: 0.273 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
REFMAC5.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.92→6.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.755 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25248 3852 5.1 %RANDOM
Rwork0.19143 ---
obs0.19446 72121 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.617 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.02 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.92→6.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6548 0 26 610 7184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226705
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.9839126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.7225879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59824.959246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.823151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1311527
X-RAY DIFFRACTIONr_chiral_restr0.2270.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025025
X-RAY DIFFRACTIONr_nbd_refined0.2610.23960
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2651
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.218
X-RAY DIFFRACTIONr_mcbond_it1.271.54506
X-RAY DIFFRACTIONr_mcangle_it1.95827059
X-RAY DIFFRACTIONr_scbond_it3.24632460
X-RAY DIFFRACTIONr_scangle_it4.2684.52067
X-RAY DIFFRACTIONr_rigid_bond_restr2.49336966
X-RAY DIFFRACTIONr_sphericity_free6.7113610
X-RAY DIFFRACTIONr_sphericity_bonded3.67236576
LS refinement shellResolution: 1.92→1.965 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 297 -
Rwork0.217 4988 -
obs--99.94 %

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