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Yorodumi- PDB-2yln: Crystal structure of the L-cystine solute receptor of Neisseria g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yln | ||||||
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Title | Crystal structure of the L-cystine solute receptor of Neisseria gonorrhoeae in the closed conformation | ||||||
Components | PUTATIVE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID | ||||||
Keywords | TRANSPORT PROTEIN / TRANSPORTER / ABC-TRANSPORTER / SOLUTE-BINDING PROTEIN | ||||||
Function / homology | Function and homology information Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | NEISSERIA GONORRHOEAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | ||||||
Authors | Bulut, H. / Moniot, S. / Scheffel, F. / Gathmann, S. / Licht, A. / Saenger, W. / Schneider, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Crystal Structures of Two Solute Receptors for L-Cystine and L-Cysteine, Respectively, of the Human Pathogen Neisseria Gonorrhoeae. Authors: Bulut, H. / Moniot, S. / Licht, A. / Scheffel, F. / Gathmann, S. / Saenger, W. / Schneider, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yln.cif.gz | 140.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yln.ent.gz | 108.9 KB | Display | PDB format |
PDBx/mmJSON format | 2yln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yln_validation.pdf.gz | 477.3 KB | Display | wwPDB validaton report |
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Full document | 2yln_full_validation.pdf.gz | 484.6 KB | Display | |
Data in XML | 2yln_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 2yln_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/2yln ftp://data.pdbj.org/pub/pdb/validation_reports/yl/2yln | HTTPS FTP |
-Related structure data
Related structure data | 2yjpC 3zsfSC 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: 30067.436 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-275 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEISSERIA GONORRHOEAE (bacteria) / Strain: FA1090 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PLYSS / References: UniProt: Q5F9M1 | ||||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | N-TERMINAL HIS-TAG CONSTRUCT WITH ENTEROKINA | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.37 Å3/Da / Density % sol: 9.4 % / Description: NONE |
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Crystal grow | pH: 4 / Details: 1.6 M AMMONIUM SULFATE, 100 MM NA-CITRATE PH 4.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→30.96 Å / Num. obs: 75069 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 7.42 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.12→1.15 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.3 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZSF Resolution: 1.12→30.96 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.964 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.232 Å2
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Refinement step | Cycle: LAST / Resolution: 1.12→30.96 Å
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Refine LS restraints |
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