+Open data
-Basic information
Entry | Database: PDB / ID: 4hzu | ||||||
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Title | Structure of a bacterial energy-coupling factor transporter | ||||||
Components |
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Keywords | HYDROLASE / TRANSPORT PROTEIN / membrane protein / ECF / transporter | ||||||
Function / homology | Function and homology information Translocases / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Lactobacillus brevis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.53 Å | ||||||
Authors | Wang, T.L. / Fu, G.B. / Pan, X.J. / Shi, Y.G. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Structure of a bacterial energy-coupling factor transporter. Authors: Wang, T. / Fu, G. / Pan, X. / Wu, J. / Gong, X. / Wang, J. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hzu.cif.gz | 390.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hzu.ent.gz | 324.8 KB | Display | PDB format |
PDBx/mmJSON format | 4hzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/4hzu ftp://data.pdbj.org/pub/pdb/validation_reports/hz/4hzu | 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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-Components
#1: Protein | Mass: 32176.533 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: ecfA1, cbiO1, LVIS_1661 / Production host: Escherichia coli (E. coli) References: UniProt: Q03PY6, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances |
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#2: Protein | Mass: 30550.432 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: ecfA2, cbiO2, LVIS_1662 / Production host: Escherichia coli (E. coli) References: UniProt: Q03PY5, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances |
#3: Protein | Mass: 30321.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: ecfT, LVIS_1660 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03PY7 |
#4: Protein | Mass: 17409.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: LVIS_2151 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03NM0 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.16 Å3/Da / Density % sol: 70.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 17% (w/v) polyethylene glycol 2000, 16% (v/v) glycerol, 100 mM Tris buffer (pH 8.2), and 100 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97947 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2012 |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 3.53→48.685 Å / Num. obs: 22601 / % possible obs: 96.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 124.93 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 3.53→3.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 1.4 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.53→48.685 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 32.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.53→48.685 Å
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Refine LS restraints |
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LS refinement shell |
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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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