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Yorodumi- PDB-1nqf: OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, METHION... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nqf | ||||||
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Title | OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, METHIONINE SUBSTIUTION CONSTRUCT FOR SE-MET SAD PHASING | ||||||
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 / porin activity / pore complex / transmembrane transporter 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 / SAD/direct method / Resolution: 2.7 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 | 1nqf.cif.gz | 123.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nqf.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nqf_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1nqf_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1nqf_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 1nqf_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/1nqf ftp://data.pdbj.org/pub/pdb/validation_reports/nq/1nqf | HTTPS FTP |
-Related 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: 66669.500 Da / Num. of mol.: 1 / Mutation: W317M, K319M, T321M, W516M, I518M, Y520M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: btuB / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(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: 3.27 Å3/Da / Density % sol: 62.36 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: PEG3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHELYENE, tris-(2-carboxyethyl)phosphine hydrochloride , 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: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Mar 5, 2002 / Details: Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal sagittal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 44260 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.085 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.7 % / Num. unique all: 3915 / Rsym value: 0.536 / % possible all: 84.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 44020 / % possible obs: 96.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.78 Å / % possible obs: 89.3 % / Rmerge(I) obs: 0.56 |
-Processing
Software |
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Refinement | Method to determine structure: SAD/direct method / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.879 / SU B: 17.389 / SU ML: 0.366 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.66 / ESU R Free: 0.357 / 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: 39.163 Å2
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Refine analyze | Luzzati sigma a free: 0.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 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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Software | *PLUS Version: 5.1.24 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.286 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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