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Yorodumi- PDB-3ftj: Crystal structure of the periplasmic region of MacB from Actinoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ftj | ||||||
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Title | Crystal structure of the periplasmic region of MacB from Actinobacillus actinomycetemcomitans | ||||||
Components | Macrolide export ATP-binding/permease protein macB | ||||||
Keywords | HYDROLASE / macrolide-specific pump / ABC-type transporter / heat stable exotoxin II / membrane protein / periplasmic region / Antibiotic resistance / ATP-binding / Cell inner membrane / Cell membrane / Membrane / Nucleotide-binding / Transmembrane / Transport | ||||||
Function / homology | Function and homology information Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Actinobacillus actinomycetemcomitans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.999 Å | ||||||
Authors | Xu, Y. / Ha, N.C. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Crystal structure of the periplasmic region of MacB, a noncanonic ABC transporter Authors: Xu, Y. / Sim, S.-H. / Nam, K.H. / Jin, X.L. / Kim, H.-M. / Hwang, K.Y. / Lee, K. / Ha, N.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ftj.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ftj.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ftj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/3ftj ftp://data.pdbj.org/pub/pdb/validation_reports/ft/3ftj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE FULL-LENGTH MACB WAS CONFIRMED AS A HOMODIMER. HOWEVER, ONLY THE PERIPLASMIC REGION BEHAVED AS A MONOMER ON A SIZE EXCLUSION CHROMATOGRAPHY, PERFORMED BY THE DEPOSITORS RESEARCH GROUP. THUS THEY SPECULATE THAT THE DIMERIC FORMATION OF FULL-LENGTH MACB IS RESPONSIBLE FOR THE CYTOPLASMIC NBD OR THE TRANSMEMBRANE SEGMENT. |
-Components
#1: Protein | Mass: 24726.875 Da / Num. of mol.: 1 / Fragment: periplasmic region, UNP residues 293-518 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinobacillus actinomycetemcomitans (bacteria) Gene: macB, MACB_ACTAC / Plasmid: pPROEX-HTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q2EHL8, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.13 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 1% PEG 400, 2.0M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. all: 14360 / Num. obs: 13829 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 17.6 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1075 / Rsym value: 0.321 / % possible all: 76 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.999→33.158 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / Data cutoff high absF: 47369.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.12 / σ(I): 0 / Phase error: 24.77 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.295 Å2 / ksol: 0.376 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.29 Å2 / Biso mean: 31.375 Å2 / Biso min: 13.11 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.999→33.158 Å
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Refine LS restraints |
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LS refinement shell |
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Xplor file |
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