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- PDB-5fp2: Crystal structure of the siderophore receptor PirA from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 5fp2
TitleCrystal structure of the siderophore receptor PirA from Pseudomonas aeruginosa
Components(FERRIC ENTEROBACTIN RECEPTOR PIRA) x 2
KeywordsMETAL TRANSPORT / TONB-DEPENDENT RECEPTOR / SIDEROPHORE RECEPTOR / OUTER-MEMBRANE PROTEIN
Function / homology
Function and homology information


siderophore transmembrane transport / siderophore transport / siderophore uptake transmembrane transporter activity / enterobactin transport / enterobactin transmembrane transporter activity / porin activity / pore complex / cell outer membrane / iron ion transport / 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
N-OCTANE / Ferric enterobactin receptor PirA
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 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
DepositionNov 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 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. SHEET DETERMINATION METHOD: DSSP 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: FERRIC ENTEROBACTIN RECEPTOR PIRA
B: FERRIC ENTEROBACTIN RECEPTOR PIRA
X: FERRIC ENTEROBACTIN RECEPTOR PIRA
Z: FERRIC ENTEROBACTIN RECEPTOR PIRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,1949
Polymers160,6594
Non-polymers5355
Water00
1
A: FERRIC ENTEROBACTIN RECEPTOR PIRA
X: FERRIC ENTEROBACTIN RECEPTOR PIRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4443
Polymers80,3302
Non-polymers1141
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FERRIC ENTEROBACTIN RECEPTOR PIRA
Z: FERRIC ENTEROBACTIN RECEPTOR PIRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7506
Polymers80,3302
Non-polymers4214
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)183.120, 95.280, 131.830
Angle α, β, γ (deg.)90.00, 127.52, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6931, -0.3621, 0.6233), (-0.3804, -0.5508, -0.7429), (0.6124, -0.752, 0.244)
Vector: -13.3908, 79.8454, 54.6541)

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Components

#1: Protein FERRIC ENTEROBACTIN RECEPTOR PIRA / IRON TRANSPORT OUTER MEMBRANE RECEPTOR


Mass: 79460.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET20B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I527
#2: Protein/peptide FERRIC ENTEROBACTIN RECEPTOR PIRA / IRON TRANSPORT OUTER MEMBRANE RECEPTOR


Mass: 869.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PEPTIDE THOUGHT PART OF THE MAIN PROTEIN CHAIN BUT CANNOT BE CONFIRMED.
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET20B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7 / Details: 17% PEG 3350, 0.2 M MGCL2, 0.1 M TRIS PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.97→52.49 Å / Num. obs: 36861 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 2.97→3.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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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: 2.97→52.49 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.853 / SU B: 59.586 / SU ML: 0.479 / Cross valid method: THROUGHOUT / ESU R: 1.508 / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.31861 1756 4.8 %RANDOM
Rwork0.26259 ---
obs0.26529 35103 98.76 %-
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: 126.995 Å2
Baniso -1Baniso -2Baniso -3
1--5.44 Å20 Å2-0.52 Å2
2--8.88 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.97→52.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8167 0 34 0 8201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198346
X-RAY DIFFRACTIONr_bond_other_d0.0020.027844
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.95911294
X-RAY DIFFRACTIONr_angle_other_deg0.71317983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.09851030
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08223.728389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.022151353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.581571
X-RAY DIFFRACTIONr_chiral_restr0.0750.21249
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0219492
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021951
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
LS refinement shellResolution: 2.97→3.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 147 -
Rwork0.373 2593 -
obs--99.93 %
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)
16.35051.42163.55594.78810.14986.1399-0.12090.15540.16050.06140.02730.1413-0.27510.1240.09361.83510.0365-0.04660.5093-0.03871.732829.79532.684.161
23.38592.3098-2.47657.046-7.277610.6325-0.02910.4181-0.0694-0.2335-0.0418-0.13880.06260.03320.07091.60760.0017-0.05010.5794-0.10851.587223.51620.03872.275
31.83710.63452.30723.24580.5242.99890.26810.0502-0.15920.325-0.2853-0.18190.14970.27590.01711.8951-0.096-0.12940.72740.00621.751434.65617.21192.964
40.70440.95331.41194.05050.01545.36390.0283-0.4099-0.08330.15760.07150.2259-0.8635-0.2504-0.09992.2686-0.2442-0.13341.1531-0.11381.74532.43438.441104.393
54.3418-1.96860.61022.5128-0.8083.2956-0.1724-0.0422-0.07120.264-0.1206-0.1372-0.3930.62630.29311.9373-0.1872-0.09760.5968-0.14981.731642.0438.92588.765
62.53650.93891.64263.06640.51083.7831-0.1558-0.32250.02340.2003-0.0542-0.0323-0.33970.09180.20991.78550.1301-0.06750.5342-0.01341.666523.12241.70170.746
74.82211.82181.89549.4103-1.86784.70410.0007-0.11910.2116-0.16130.18760.2815-0.2769-0.1079-0.18831.7669-0.0391-0.0420.4375-0.03531.58925.74-12.44567.633
82.775-0.7081-7.35851.43241.446819.7596-0.1127-0.24010.0914-0.2104-0.0435-0.15540.35760.43380.15622.0102-0.0656-0.00181.635-0.07161.89361.083-7.39181.514
91.01580.78321.9782.56931.06633.9848-0.137-0.1022-0.0137-0.06970.0750.0945-0.177-0.1660.0621.8252-0.00810.06290.39570.00011.70038.531-0.41271.423
101.8723-0.22710.72122.83410.39341.8240.0882-0.1623-0.1010.2626-0.054-0.05740.0377-0.3723-0.03421.851-0.0726-0.04230.56030.06461.684713.166-14.02384.759
110.7884-0.5834-2.57682.39291.57168.63680.1568-0.0228-0.1220.2427-0.26360.3789-0.03480.07390.10681.7735-0.0944-0.1350.8570.02911.896-3.815-24.12276.64
122.4534-0.29481.61113.83310.22823.2509-0.15670.088-0.1966-0.18890.13480.22690.02060.0960.02191.7150.0742-0.04660.48610.01851.5890.018-5.87954.332
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 160
2X-RAY DIFFRACTION2A161 - 244
3X-RAY DIFFRACTION3A245 - 421
4X-RAY DIFFRACTION4A422 - 467
5X-RAY DIFFRACTION5A468 - 585
6X-RAY DIFFRACTION6A586 - 715
7X-RAY DIFFRACTION7B32 - 103
8X-RAY DIFFRACTION8B104 - 127
9X-RAY DIFFRACTION9B128 - 241
10X-RAY DIFFRACTION10B242 - 445
11X-RAY DIFFRACTION11B446 - 573
12X-RAY DIFFRACTION12B574 - 715

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