+Open data
-Basic information
Entry | Database: PDB / ID: 1nqe | ||||||
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Title | OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI | ||||||
Components | Vitamin B12 receptor | ||||||
Keywords | TRANSPORT PROTEIN / BETA BARREL / cobalamin / VITAMIN B12 / OUTER MEMBRANE TRANSPORT | ||||||
Function / homology | Function and homology information ABC-type vitamin B12 transporter activity / cobalamin transport / transmembrane transporter complex / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / protein domain specific binding / calcium ion binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chimento, D.P. / Mohanty, A.K. / Kadner, R.J. / Wiener, M.C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Substrate-induced transmembrane signaling in the cobalamin transporter BtuB Authors: Chimento, D.P. / Mohanty, A.K. / Kadner, R.J. / Wiener, M.C. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization and initial X-ray diffraction of BtuB, the integral membrane cobalamin transporter of Escherichia coli Authors: Chimento, D.P. / Mohanty, A.K. / Kadner, R.J. / Wiener, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nqe.cif.gz | 133.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nqe.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/1nqe ftp://data.pdbj.org/pub/pdb/validation_reports/nq/1nqe | HTTPS FTP |
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-Related structure data
Related structure data | 1nqfSC 1nqgC 1nqhC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 66386.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: btuB / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P06129 | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-C8E / ( #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.54 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: PEG 3350, magnesium acetate, bis-tris, n-octyl tetraoxyethylene , pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Chimento, D.P., (2003) Acta Crystallogr., Sect.D, 59, 509. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 26, 2000 / Details: Rh-coated Si mirror |
Radiation | Monochromator: Bent triangular asymmetric cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 56085 / Num. obs: 55698 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rsym value: 0.065 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.69 / Num. unique all: 5362 / Rsym value: 0.412 / % possible all: 97.8 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 55620 / % possible obs: 99.6 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.18 Å / % possible obs: 97.8 % / Rmerge(I) obs: 0.412 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NQF Resolution: 2→24.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.83 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.142 / Stereochemistry target values: Engh & Huber Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE AVERAGE ISOTROPIC B VALUE IS AN AVERAGE RESIDUAL B FACTOR.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.151 Å2
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Refine analyze | Luzzati sigma a free: 0.142 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→24.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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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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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.194 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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