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- PDB-4kyd: Partial Structure of the C-terminal domain of the HPIV4B phosphop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kyd | |||||||||
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Title | Partial Structure of the C-terminal domain of the HPIV4B phosphoprotein, fused to MBP. | |||||||||
![]() | Maltose-binding periplasmic protein, Phosphoprotein, chimeric construct | |||||||||
![]() | binding protein / viral protein / 3 helix bundle / viral nucleocapsid | |||||||||
Function / homology | ![]() detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Yegambaram, K. / Bulloch, E.M.M. / Kingston, R.L. | |||||||||
![]() | ![]() Title: Protein domain definition should allow for conditional disorder. Authors: Yegambaram, K. / Bulloch, E.M. / Kingston, R.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 327 KB | Display | ![]() |
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PDB format | ![]() | 268.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 44.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kycC ![]() 4kyeC ![]() 1hsjS C: citing same article ( S: Starting model for refinement |
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Similar 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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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | AUTHOR REMARK. IN SOLUTION THE C-TERMINAL DOMAIN OF THE HPIV4B PHOSPHOPROTEIN FORMS A MONOMERIC 3-HELIX BUNDLE. IN THE CRYSTAL, DISPLACEMENT OF THE FINAL HELIX AND PARTIAL REPACKING OF THE HYDROPHOBIC CORE LEAD TO FORMATION OF A HOMO-DIMERIC 4-HELIX BUNDLE. WE HAVE FOUND NO EVIDENCE THAT THIS HOMO-DIMER PERSISTS IN SOLUTION. SEE PRIMARY CITATION |
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Components
#1: Protein | Mass: 45953.973 Da / Num. of mol.: 2 Fragment: unp P0AEX9 residues 27-392, unp P21738 residues 351-399 Mutation: D82A,K83A, E359A, K362A, D363A, C368S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12, 68-333 Strain / Gene: b4034, JW3994, malE, P, P/V / Plasmid: pMAL(A) / Production host: ![]() ![]() #2: Polysaccharide | #3: Chemical | ChemComp-MPO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 24 %(w/v) PEG 2000 0.2 M MOPS/KOH, pH 7.30, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 23, 2001 / Details: Osmic mirror optics |
Radiation | Monochromator: Rigaku Varimax HF confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→38.1 Å / Num. all: 43158 / Num. obs: 43158 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.21→2.25 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.7 / % possible all: 82.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB accession code 1HSJ Resolution: 2.21→38.1 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.274 / SU ML: 0.137 Isotropic thermal model: 1 TLS group per protein molecule + Residual Isotropic B-Factors Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 54.365 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→38.1 Å
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Refine LS restraints |
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