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- PDB-3d9x: Structure of the head of the Bartonella adhesin BadA -

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Basic information

Entry
Database: PDB / ID: 3d9x
TitleStructure of the head of the Bartonella adhesin BadA
ComponentsAdhesin A
KeywordsCELL ADHESION / BadA / trimeric Adhesin / structure modules / high resolution
Function / homology
Function and homology information


cell outer membrane / protein transport / cell adhesion / cell surface
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2120 / N-terminal domain of TfIIb - #100 / Ubiquitin Ligase Nedd4; Chain: W; - #140 / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / N-terminal domain of TfIIb ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2120 / N-terminal domain of TfIIb - #100 / Ubiquitin Ligase Nedd4; Chain: W; - #140 / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / N-terminal domain of TfIIb / Ubiquitin Ligase Nedd4; Chain: W; / Pilin-like / Serralysin-like metalloprotease, C-terminal / Other non-globular / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single Sheet / Helix non-globular / Special / Mainly Beta
Similarity search - Domain/homology
Autotransporter adhesin BadA
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsZeth, K. / Lupas, A. / Martin, J.
CitationJournal: Plos Pathog. / Year: 2008
Title: Structure of the head of the Bartonella adhesin BadA
Authors: Szczesny, P. / Linke, D. / Ursinus, A. / Bar, K. / Schwarz, H. / Riess, T.M. / Kempf, V.A. / Lupas, A.N. / Martin, J. / Zeth, K.
History
DepositionMay 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Adhesin A
B: Adhesin A
C: Adhesin A


Theoretical massNumber of molelcules
Total (without water)51,5953
Polymers51,5953
Non-polymers00
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15170 Å2
ΔGint-86 kcal/mol
Surface area14790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.870, 51.140, 58.620
Angle α, β, γ (deg.)65.87, 76.60, 82.08
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Adhesin A


Mass: 17198.182 Da / Num. of mol.: 3 / Fragment: BadA adhesin head fragment, UNP residues 374-536
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: badA / Production host: Escherichia coli (E. coli) / References: UniProt: Q5MWV9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 1.538955 Å3/Da / Density % sol: 20.075651 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M ammonium sulfate, 0.05M Bis-Tris (pH 6.5), 30% v/v pentaerythrol ethoxylate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→30 Å / Num. obs: 105179 / % possible obs: 90.7 % / Observed criterion σ(I): 3.7 / Redundancy: 5.8 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 3.7
Reflection shellResolution: 1.13→1.16 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.7 / Num. unique all: 14273 / % possible all: 76

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1s7m

1s7m


Resolution: 1.13→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.875 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.037 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17801 5256 5 %RANDOM
Rwork0.15592 ---
all0.157 105179 --
obs0.15704 99858 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.076 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.22 Å2-0.15 Å2
2---0.09 Å20.23 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.13→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2584 0 0 422 3006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222623
X-RAY DIFFRACTIONr_bond_other_d0.0010.021710
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9613579
X-RAY DIFFRACTIONr_angle_other_deg0.82934301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1775381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.228.113106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18215495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.203154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022996
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02433
X-RAY DIFFRACTIONr_nbd_refined0.2110.2532
X-RAY DIFFRACTIONr_nbd_other0.1910.21882
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21343
X-RAY DIFFRACTIONr_nbtor_other0.0840.21491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1880.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.258
X-RAY DIFFRACTIONr_mcbond_it1.7691.52343
X-RAY DIFFRACTIONr_mcbond_other0.4711.5740
X-RAY DIFFRACTIONr_mcangle_it2.00522795
X-RAY DIFFRACTIONr_scbond_it2.62331040
X-RAY DIFFRACTIONr_scangle_it3.4194.5760
X-RAY DIFFRACTIONr_rigid_bond_restr1.34535319
X-RAY DIFFRACTIONr_sphericity_free4.4293432
X-RAY DIFFRACTIONr_sphericity_bonded2.52134294
LS refinement shellResolution: 1.13→1.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 278 -
Rwork0.208 5272 -
obs--100 %

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