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- PDB-5fr8: Crystal structure of the siderophore receptor PirA from Acinetoba... -

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Basic information

Entry
Database: PDB / ID: 5fr8
TitleCrystal structure of the siderophore receptor PirA from Acinetobacter baumannii
ComponentsTONB-DEPENDENT SIDEROPHORE RECEPTOR
KeywordsTRANSPORT PROTEIN / TONB-DEPENDENT RECEPTOR / OUTER-MEMBRANE PROTEIN
Function / homology
Function and homology information


siderophore uptake transmembrane transporter activity / porin activity / pore complex / cell outer membrane / signaling receptor activity
Similarity search - Function
TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily ...TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Probable TonB-dependent siderophore receptor PirA
Similarity search - Component
Biological speciesACINETOBACTER BAUMANNII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsMoynie, L. / Tortajada, A. / Naismith, J.H.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Structure and Function of the PiuA and PirA Siderophore-Drug Receptors from Pseudomonas aeruginosa and Acinetobacter baumannii.
Authors: Moynie, L. / Luscher, A. / Rolo, D. / Pletzer, D. / Tortajada, A. / Weingart, H. / Braun, Y. / Page, M.G. / Naismith, J.H. / Kohler, T.
History
DepositionDec 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TONB-DEPENDENT SIDEROPHORE RECEPTOR
B: TONB-DEPENDENT SIDEROPHORE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,8004
Polymers161,1882
Non-polymers6132
Water543
1
A: TONB-DEPENDENT SIDEROPHORE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9002
Polymers80,5941
Non-polymers3061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TONB-DEPENDENT SIDEROPHORE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9002
Polymers80,5941
Non-polymers3061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.090, 99.090, 504.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 24 - 730 / Label seq-ID: 27 - 733

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.4995, -0.8662, 0.0147), (-0.8662, 0.4996, 0.0102), (-0.0161, -0.0076, -0.9998)
Vector: -40.3072, 0.0658, 84.113)

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Components

#1: Protein TONB-DEPENDENT SIDEROPHORE RECEPTOR / IRON TRANSPORT OUTER MEMBRANE RECEPTOR


Mass: 80593.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACINETOBACTER BAUMANNII (bacteria) / Plasmid: PTAMAHISTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: D0C8V9
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.44 Å3/Da / Density % sol: 72 % / Description: NONE
Crystal growpH: 9 / Details: 16% PEG 8000, 0.15 M MAGNESIUM SULFATE BICINE PH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.919
11-h,-k,l20.081
ReflectionResolution: 2.83→85.81 Å / Num. obs: 62752 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.5
Reflection shellResolution: 2.83→2.98 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.4 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
XDSdata reduction
xia2data scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FEP

1fep


Resolution: 2.83→84.6 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.891 / SU B: 24.586 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25795 3157 5 %RANDOM
Rwork0.22745 ---
obs0.22901 59594 89.34 %-
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: 69.82 Å2
Baniso -1Baniso -2Baniso -3
1--5.27 Å20 Å20 Å2
2---5.27 Å20 Å2
3---10.53 Å2
Refinement stepCycle: LAST / Resolution: 2.83→84.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10950 0 42 3 10995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211184
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210434
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.94915120
X-RAY DIFFRACTIONr_angle_other_deg0.727324016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20851412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24425.037540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.146151906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0191568
X-RAY DIFFRACTIONr_chiral_restr0.0750.21646
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213012
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022596
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 41729 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.83→2.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 231 -
Rwork0.309 4455 -
obs--91.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.67340.1438-0.47292.9343-1.0531.8610.0555-0.5381-0.3635-0.0455-0.1059-0.1194-0.07610.12930.05040.16250.00760.00350.3567-0.06970.3606-14.158-35.16475.124
23.65052.3833-0.90032.7006-0.53161.09480.3261-0.7824-0.1540.2281-0.3668-0.013-0.2260.10370.04070.30230.0136-0.01970.5529-0.08920.3309-23.442-31.33487.974
31.92120.1766-0.36951.3961-0.63361.4007-0.0360.09180.0631-0.38650.13320.161-0.1053-0.3126-0.09720.25380.05350.01940.3538-0.12810.4662-27.512-28.7867.51
41.97880.8062-0.94391.22870.43661.2731-0.2104-0.0109-0.4546-0.20710.0018-0.30040.1249-0.04850.20850.3289-0.00420.11990.2948-0.12520.5846-10.664-41.68561.627
53.1192.3857-0.55113.0514-2.90185.5325-0.1430.58150.4091-0.2950.44480.4566-0.1152-0.2969-0.30180.69060.11690.02570.6005-0.03820.5447-22.367-12.91445.077
61.7708-0.0262-0.10791.4302-0.52192.13880.0753-0.6193-0.13470.2254-0.241-0.353-0.23810.32240.16570.2276-0.1145-0.00650.4537-0.09340.5058-1.693-27.11478.634
71.91310.5631-0.04851.6822-0.3021.1589-0.35040.4384-0.2074-0.35760.2437-0.28630.2768-0.12510.10670.4352-0.26730.19840.1968-0.15470.594517.122-38.7915.509
82.27550.7488-0.87390.99160.05842.2825-0.23910.5578-0.0681-0.36360.2028-0.0985-0.277-0.37160.03620.5394-0.22050.17140.2363-0.10140.689318.612-27.5473.693
911.81371.7086-3.53120.67640.04383.7731-0.07220.210.1863-0.14140.1046-0.0499-0.5704-0.4616-0.03240.4036-0.0540.09570.2047-0.09840.419210.053-18.86316.35
102.104-0.984-0.8421.81790.41131.6995-0.1193-0.1602-0.26060.0613-0.0307-0.31230.1190.22730.14990.325-0.14540.12710.1533-0.06150.628125.345-38.18123.752
111.5844-0.7245-0.67943.12071.92972.5871-0.3841-0.2128-0.1680.44110.3748-0.19420.34330.10630.00930.455-0.12460.18970.2027-0.04810.540113.096-41.66525.866
121.7154-0.2347-0.32021.62920.63181.199-0.35020.3598-0.2703-0.16890.13640.14990.1042-0.31370.21380.4049-0.28940.16750.2826-0.13280.6224.326-45.0438.562
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 157
2X-RAY DIFFRACTION2A158 - 252
3X-RAY DIFFRACTION3A253 - 408
4X-RAY DIFFRACTION4A409 - 537
5X-RAY DIFFRACTION5A538 - 570
6X-RAY DIFFRACTION6A571 - 730
7X-RAY DIFFRACTION7B24 - 191
8X-RAY DIFFRACTION8B192 - 313
9X-RAY DIFFRACTION9B314 - 348
10X-RAY DIFFRACTION10B349 - 492
11X-RAY DIFFRACTION11B493 - 557
12X-RAY DIFFRACTION12B558 - 730

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