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- PDB-6h7f: Crystal structure of BauA, the Ferric preacinetobactin receptor f... -

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Basic information

Entry
Database: PDB / ID: 6h7f
TitleCrystal structure of BauA, the Ferric preacinetobactin receptor from Acinetobacter baumannii in complex with Fe3+-Preacinetobactin-acinetobactin
ComponentsBauAFederal Institute for Occupational Safety and Health
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 / 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
: / Chem-FV8 / Chem-OPV / Chem-OPZ / BauA
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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
DepositionJul 31, 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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)242,88184
Polymers229,0403
Non-polymers13,84181
Water13,547752
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26310 Å2
ΔGint203 kcal/mol
Surface area76230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.640, 220.650, 101.140
Angle α, β, γ (deg.)90.00, 99.09, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / 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

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Protein , 1 types, 3 molecules ABC

#1: Protein BauA / Federal Institute for Occupational Safety and Health / 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

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Non-polymers , 7 types, 833 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-FV8 / (4~{S},5~{R})-2-[2,3-bis(oxidanyl)phenyl]-~{N}-[2-(1~{H}-imidazol-4-yl)ethyl]-5-methyl-~{N}-oxidanyl-4,5-dihydro-1,3-oxazole-4-carboxamide


Mass: 346.338 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H18N4O5
#4: Chemical ChemComp-OPV / ~{N}-[(4~{S},5~{S})-2-[2-(1~{H}-imidazol-4-yl)ethyl]-5-methyl-3-oxidanylidene-1,2-oxazolidin-4-yl]-2,3-bis(oxidanyl)benzamide


Mass: 346.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N4O5
#5: Chemical ChemComp-OPZ / ~{N}-[(4~{S},5~{R})-2-[2-(1~{H}-imidazol-4-yl)ethyl]-5-methyl-3-oxidanylidene-1,2-oxazolidin-4-yl]-2,3-bis(oxidanyl)benzamide


Mass: 346.338 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H18N4O5
#6: Chemical...
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 752 / 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: 4.32 Å3/Da / Density % sol: 71.53 %
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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.26→49.93 Å / Num. obs: 180631 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.108 / Net I/σ(I): 9.2
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 9050 / CC1/2: 0.527 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6h7v

6h7v


Resolution: 2.26→49.93 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21689 8832 4.9 %RANDOM
Rwork0.18648 ---
obs0.18795 171799 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å21.22 Å2
2---0.73 Å20 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.26→49.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15402 0 683 752 16837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01416741
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714962
X-RAY DIFFRACTIONr_angle_refined_deg0.9581.69622599
X-RAY DIFFRACTIONr_angle_other_deg0.8121.72435089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.01652084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34123.529768
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.869152499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1031563
X-RAY DIFFRACTIONr_chiral_restr0.0510.22140
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218770
X-RAY DIFFRACTIONr_gen_planes_other00.023142
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_it3.953.6318255
X-RAY DIFFRACTIONr_mcbond_other3.953.6318256
X-RAY DIFFRACTIONr_mcangle_it4.9355.44710366
X-RAY DIFFRACTIONr_mcangle_other4.9365.44710367
X-RAY DIFFRACTIONr_scbond_it5.9234.348486
X-RAY DIFFRACTIONr_scbond_other5.9234.348486
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9846.22912234
X-RAY DIFFRACTIONr_long_range_B_refined8.93142.39116953
X-RAY DIFFRACTIONr_long_range_B_other8.9342.39316954
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)
11A217940.06
12B217940.06
21A216300.07
22C216300.07
31B216030.07
32C216030.07
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 590 -
Rwork0.312 12702 -
obs--99.86 %

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