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- PDB-2x4l: Crystal structure of DesE, a ferric-siderophore receptor protein ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x4l | ||||||
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Title | Crystal structure of DesE, a ferric-siderophore receptor protein from Streptomyces coelicolor | ||||||
![]() | FERRIC-SIDEROPHORE RECEPTOR PROTEIN | ||||||
![]() | TRANSPORT | ||||||
Function / homology | ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / outer membrane-bounded periplasmic space / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Secreted protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H. | ||||||
![]() | ![]() Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.2 KB | Display | ![]() |
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PDB format | ![]() | 100.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ivyC ![]() 2jg5C ![]() 2jg6C ![]() 2vw8C ![]() 2vxzC ![]() 2wj9C ![]() 2x0oC ![]() 2x3dC ![]() 2x3eC ![]() 2x3fC ![]() 2x3gC ![]() 2x3lC ![]() 2x3mC ![]() 2x3nC ![]() 2x3oC ![]() 2x48C ![]() 2x4gC ![]() 2x4hC ![]() 2x4iC ![]() 2x4jC ![]() 2x4kC ![]() 2x5cC ![]() 2x5dC ![]() 2x5fC ![]() 2x5gC ![]() 2x5hC ![]() 2x5pC ![]() 2x5qC ![]() 2x5rC ![]() 2x5tC ![]() 2x7bC ![]() 2x7iC ![]() 2xu2C 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
#1: Protein | Mass: 34575.973 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-349 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.77 % / Description: NONE |
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Crystal grow | pH: 6 Details: FROM 2.63M SODIUM MALONATE, 0.1M BISTRIS PH 6.0, 0.24M NACL. CRYSTAL WAS CRYOPROTECTED BY 3.4M SODIUM MALONATE, 0.1M BISTRIS PH 6.0, 0.25M NACL. PHASES WERE DETERMINED BY SOAKING CRYSTAL IN ...Details: FROM 2.63M SODIUM MALONATE, 0.1M BISTRIS PH 6.0, 0.24M NACL. CRYSTAL WAS CRYOPROTECTED BY 3.4M SODIUM MALONATE, 0.1M BISTRIS PH 6.0, 0.25M NACL. PHASES WERE DETERMINED BY SOAKING CRYSTAL IN 2.8M SODIUM MALONATE, 0.1M BISTRIS PH 6.0, 0.5M NABR FOR 1 MINUTE PRIOR TO CRYOPROTECTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 29, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 50077 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.17 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.5→29.48 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.602 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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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 mean: 10.161 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.48 Å
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Refine LS restraints |
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