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- PDB-7f6u: Crystal structure of metal-citrate-binding mutant (Y221A) protein... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7f6u | ||||||
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Title | Crystal structure of metal-citrate-binding mutant (Y221A) protein (MctA) of ABC transporter in apo state | ||||||
![]() | Iron ABC transporter, periplasmic iron-binding protein | ||||||
![]() | TRANSPORT PROTEIN / Substrate-binding protein / metal ion / secondary transporter / symporter | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kanaujia, S.P. / Mandal, S.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and thermodynamic insights into a novel Mg 2+ -citrate-binding protein from the ABC transporter superfamily. Authors: Mandal, S.K. / Kanaujia, S.P. #1: ![]() Title: Structural and thermodynamic insights into a novel Mg2+-citrate-binding protein from the ABC transporter superfamily Authors: Mandal, S.K. / Kanaujia, S.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.6 KB | Display | ![]() |
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PDB format | ![]() | 122.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 508.3 KB | Display | ![]() |
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Full document | ![]() | 516.4 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7f6eSC ![]() 7f6fC ![]() 7f6kC ![]() 7f6nC ![]() 7f6oC ![]() 7f6pC ![]() 7f6qC ![]() 7f6rC ![]() 7f6sC ![]() 7f6tC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38091.316 Da / Num. of mol.: 1 / Mutation: Y221A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHB177 / Plasmid: pET22b / Production host: ![]() ![]() |
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-Non-polymers , 9 types, 293 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/BGQ.gif)
![](data/chem/img/1MI.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/BGQ.gif)
![](data/chem/img/1MI.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-CO2 / | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-BGQ / | #8: Chemical | ChemComp-1MI / | #9: Chemical | ChemComp-CAC / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.87 % / Description: Orthorhombic |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 9, 2019 / Details: VariMax HF | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→54.3 Å / Num. obs: 40385 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.032 / Rrim(I) all: 0.093 / Net I/σ(I): 13.2 / Num. measured all: 324728 / Scaling rejects: 159 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7F6E Resolution: 1.75→48.68 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.76 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.82 Å2 / Biso mean: 29.588 Å2 / Biso min: 13.29 Å2
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Refinement step | Cycle: final / Resolution: 1.75→48.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 4.8149 Å / Origin y: 37.0978 Å / Origin z: 28.8343 Å
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