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Yorodumi- PDB-4n0q: Crystal Structure of an ABC transporter, substrate-binding protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n0q | ||||||
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Title | Crystal Structure of an ABC transporter, substrate-binding protein from Brucella melitensis 16M in complex with L-Leucine using a crystal grown in a Crystal Former (Microlytic) | ||||||
Components | Leu/Ile/Val-binding protein homolog 3 | ||||||
Keywords | TRANSPORT PROTEIN / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / ABC transporter / amino-acid transport | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Brucella melitensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of an ABC transporter, substrate-binding protein from Brucella melitensis 16M in complex with L-Leucine using a crystal grown in a Crystal Former (Microlytic) Authors: Dranow, D.M. / Edwards, T.E. / Lorimer, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n0q.cif.gz | 474.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n0q.ent.gz | 392.8 KB | Display | PDB format |
PDBx/mmJSON format | 4n0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n0q_validation.pdf.gz | 472.8 KB | Display | wwPDB validaton report |
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Full document | 4n0q_full_validation.pdf.gz | 479.8 KB | Display | |
Data in XML | 4n0q_validation.xml.gz | 50.9 KB | Display | |
Data in CIF | 4n0q_validation.cif.gz | 73.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/4n0q ftp://data.pdbj.org/pub/pdb/validation_reports/n0/4n0q | HTTPS FTP |
-Related structure data
Related structure data | 3ipcS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 36725.395 Da / Num. of mol.: 4 / Fragment: UNP residues 23-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEI1930 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YEE8 #2: Chemical | ChemComp-LEU / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.24 % |
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Crystal grow | Temperature: 294 K / Method: microfluidic / pH: 5.5 Details: SuperCOMBI(b4): 0.2 M magnesium chloride, 0.1 M Bis-Tris-HCl, pH 5.5, 25% PEG3350, MICROFLUIDIC, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 6, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. all: 54462 / Num. obs: 53389 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.67 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IPC Resolution: 2.3→19.93 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 0.32 / SU B: 14.24 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.519 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.747 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.93 Å
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Refine LS restraints |
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