+Open data
-Basic information
Entry | Database: PDB / ID: 8b43 | ||||||
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Title | Crystal structure of ferrioxamine transporter | ||||||
Components | Ferrichrome-iron receptor | ||||||
Keywords | MEMBRANE PROTEIN / Siderophore TonB-dependent transporter Pseudomonas aeruginosa Iron | ||||||
Function / homology | Function and homology information siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Josts, I. / Tidow, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Interactions of TonB-dependent transporter FoxA with siderophores and antibiotics that affect binding, uptake, and signal transduction. Authors: Chan, D.C.K. / Josts, I. / Koteva, K. / Wright, G.D. / Tidow, H. / Burrows, L.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b43.cif.gz | 292.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b43.ent.gz | 234.8 KB | Display | PDB format |
PDBx/mmJSON format | 8b43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b43_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 8b43_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 8b43_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 8b43_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/8b43 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/8b43 | HTTPS FTP |
-Related structure data
Related structure data | 6i96S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 90058.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: fhuA, CAZ10_13360, CCBH4851_00003, E4V10_32510, E5Z62_12280, E5Z63_14065, ECC04_000265, IPC111_29490, IPC112_00225, IPC113_05635, IPC114_00330, IPC115_06110, IPC116_18480, IPC117_19040, IPC118_ ...Gene: fhuA, CAZ10_13360, CCBH4851_00003, E4V10_32510, E5Z62_12280, E5Z63_14065, ECC04_000265, IPC111_29490, IPC112_00225, IPC113_05635, IPC114_00330, IPC115_06110, IPC116_18480, IPC117_19040, IPC118_20600, IPC119_16420, IPC120_21950, IPC121_12885, IPC122_11180, IPC123_16730, IPC127_08885, IPC128_09865, IPC129_00020, IPC1308_04865, IPC1309_03980, IPC130_05340, IPC1316_31905, IPC1318_19180, IPC1319_31550, IPC1322_32775, IPC1323_26065, IPC1324_33040, IPC1325_29400, IPC1326_32065, IPC1327_32520, IPC1328_29370, IPC1330_28425, IPC1331_24705, IPC1334_10415, IPC1336_30070, IPC1337_10850, IPC1339_09990, IPC133_29845, IPC1340_09045, IPC1341_24180, IPC1345_29990, IPC1346_29735, IPC1348_00035, IPC1349_15780, IPC135_30075, IPC137_00035, IPC144_29610, IPC145_28630, IPC146_29610, IPC1474_04965, IPC1476_32515, IPC1477_33575, IPC1478_33300, IPC1479_32370, IPC147_29490, IPC1480_32130, IPC1481_32815, IPC1482_21280, IPC1485_09320, IPC1486_10855, IPC1487_33190, IPC1489_18290, IPC148_26420, IPC1491_08270, IPC1492_29835, IPC1495_19880, IPC1496_33380, IPC1499_32915, IPC149_29645, IPC1502_10500, IPC1505_28910, IPC1506_21665, IPC1507_22645, IPC1508_18730, IPC1509_33270, IPC150_29930, IPC1510_33310, IPC1511_32960, IPC1514_01540, IPC1515_22320, IPC1516_17155, IPC1519_22675, IPC151_29990, IPC1521_33400, IPC1522_24390, IPC1523_32260, IPC1583_30165, IPC1584_20440, IPC1585_29835, IPC1588_30170, IPC1591_33265, IPC1594_30075, IPC1598_25380, IPC1600_30275, IPC1601_29690, IPC1605_17140, IPC1606_30605, IPC161_15130, IPC162_30720, IPC163_19705, IPC164_31415, IPC165_30780, IPC166_01575, IPC167_30540, IPC168_09805, IPC169_30590, IPC170_31460, IPC171_30710, IPC172_27970, IPC173_29435, IPC174_29630, IPC175_29725, IPC176_29315, IPC177_02190, IPC179_31230, IPC180_31650, IPC181_32015, IPC182_29540, IPC183_29205, IPC184_29735, IPC30_22565, IPC31_25415, IPC32_21555, IPC56_24585, IPC574_27490, IPC575_26795, IPC576_25760, IPC577_27630, IPC578_25795, IPC579_25235, IPC580_09580, IPC582_23120, IPC584_11300, IPC586_25800, IPC589_11355, IPC603_33385, IPC604_32235, IPC605_33360, IPC606_33430, IPC608_27725, IPC609_32540, IPC610_23145, IPC611_33385, IPC612_21400, IPC613_33705, IPC614_33670, IPC615_33055, IPC616_32660, IPC618_22390, IPC61_22085, IPC620_33170, IPC624_33400, IPC70_09875, IPC72_30920, IPC73_32315, IPC74_32150, IPC75_28580, IPC77_23050, IPC78_29675 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C7CQY7 | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Sugar | #4: Chemical | #5: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.63 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: 1.8 M ammonium sulfate 0.1 M MES pH 6.5 0.7% octyl glucoside |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.489→82.628 Å / Num. obs: 20915 / % possible obs: 94.1 % / Redundancy: 18.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.043 / Rrim(I) all: 0.185 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.489→2.81 Å / Redundancy: 14.5 % / Rmerge(I) obs: 1.91 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1045 / CC1/2: 0.727 / Rpim(I) all: 0.506 / % possible all: 74.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I96 Resolution: 2.49→59.33 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 170.16 Å2 / Biso mean: 60.7225 Å2 / Biso min: 24.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.49→59.33 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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