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- PDB-4hmp: Crystal structure of iron uptake ABC transporter substrate-bindin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hmp | ||||||
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Title | Crystal structure of iron uptake ABC transporter substrate-binding protein PiaA from Streptococcus pneumoniae TIGR4 | ||||||
![]() | Iron-compound ABC transporter, iron compound-binding protein | ||||||
![]() | TRANSPORT PROTEIN / class III substrate binding protein / alpha and beta protein / periplasmic binding protein type III fold / iron uptake ABC transporter system substrate-binding protein / hydroxamate siderophore / membrane-anchored lipoprotein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cheng, W. / Li, Q. / Jiang, Y.-L. / Chen, Y. / Zhou, C.-Z. | ||||||
![]() | ![]() Title: Structures of Streptococcus pneumoniae PiaA and Its Complex with Ferrichrome Reveal Insights into the Substrate Binding and Release of High Affinity Iron Transporters Authors: Cheng, W. / Li, Q. / Jiang, Y.-L. / Zhou, C.-Z. / Chen, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123 KB | Display | ![]() |
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PDB format | ![]() | 101.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.2 KB | Display | ![]() |
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Full document | ![]() | 489.1 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36514.586 Da / Num. of mol.: 2 / Fragment: UNP residues 23-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 115 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 5.2 Details: 30% PEG 400, 0.1M NaAc, 0.1M CdCl2, pH 5.2, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 17106 / Num. obs: 17491 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 4.2 / Num. unique all: 826 / Rsym value: 0.245 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.7 Å2 / Biso mean: 27.867 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→41.12 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 24 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.701→2.771 Å / Total num. of bins used: 20
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