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- PDB-6hcp: Crystal structure of BauA, the Ferric preacinetobactin receptor f... -

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Basic information

Entry
Database: PDB / ID: 6hcp
TitleCrystal structure of BauA, the Ferric preacinetobactin receptor from Acinetobacter baumannii
ComponentsBauA
KeywordsMEMBRANE PROTEIN / BauA / outer-membrane transporter
Function / homology
Function and homology information


: / siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity
Similarity search - Function
TonB-dependent siderophore receptor FcuA/FatA / TonB-dependent receptor-like / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain
Similarity search - Domain/homology
PHOSPHATE ION / BauA
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsMoynie, L. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Elife / Year: 2018
Title: Preacinetobactin not acinetobactin is essential for iron uptake by the BauA transporter of the pathogenAcinetobacter baumannii.
Authors: Moynie, L. / Serra, I. / Scorciapino, M.A. / Oueis, E. / Page, M.G. / Ceccarelli, M. / Naismith, J.H.
History
DepositionAug 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / entity / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BauA
B: BauA
C: BauA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,267110
Polymers229,0403
Non-polymers15,227107
Water35,9401995
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, The biological assembly is unclear, SEC-MALS result is dependent of the detergent used., light scattering, The biological assembly is unclear, SEC-MALS result is dependent ...Evidence: light scattering, The biological assembly is unclear, SEC-MALS result is dependent of the detergent used., light scattering, The biological assembly is unclear, SEC-MALS result is dependent of the detergent used., light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35720 Å2
ΔGint351 kcal/mol
Surface area74330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.200, 219.520, 101.430
Angle α, β, γ (deg.)90.00, 99.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1547-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 33 - 703 / Label seq-ID: 36 - 706

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein BauA / Probable ferric acinetobactin receptor


Mass: 76346.508 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: bauA / Production host: Escherichia coli (E. coli) / References: UniProt: Q76HJ9
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 71 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical...
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1995 / 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

Crystal growTemperature: 294 K / Method: vapor diffusion / Details: PEG 8000 Hepes KCl ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.83→57.24 Å / Num. obs: 339550 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.1
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 25109 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→57.24 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.964 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17662 17140 5 %RANDOM
Rwork0.15552 ---
obs0.15659 322409 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20.74 Å2
2---0.88 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.83→57.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15402 0 733 1995 18130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01417154
X-RAY DIFFRACTIONr_bond_other_d00.01715556
X-RAY DIFFRACTIONr_angle_refined_deg1.161.6923123
X-RAY DIFFRACTIONr_angle_other_deg0.9171.7436524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04552162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4623.529782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.447152561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5211564
X-RAY DIFFRACTIONr_chiral_restr0.0610.22190
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0219209
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023195
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.313.0378462
X-RAY DIFFRACTIONr_mcbond_other3.3063.0368461
X-RAY DIFFRACTIONr_mcangle_it3.8964.53610686
X-RAY DIFFRACTIONr_mcangle_other3.8964.53610687
X-RAY DIFFRACTIONr_scbond_it5.623.7198692
X-RAY DIFFRACTIONr_scbond_other5.6153.7188689
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.45.29212432
X-RAY DIFFRACTIONr_long_range_B_refined8.63338.23818088
X-RAY DIFFRACTIONr_long_range_B_other8.44836.99217364
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A223450.06
12B223450.06
21A221150.07
22C221150.07
31B220870.07
32C220870.07
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 1268 -
Rwork0.251 23807 -
obs--99.58 %

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