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Yorodumi- PDB-3zsf: Crystal structure of the L-cystine solute receptor of Neisseria g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zsf | ||||||
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Title | Crystal structure of the L-cystine solute receptor of Neisseria gonorrhoeae in the unliganded open conformation | ||||||
Components | ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACIDATP-binding cassette transporter | ||||||
Keywords | TRANSPORT 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: 2.32 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 | 3zsf.cif.gz | 710.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zsf.ent.gz | 590.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zsf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/3zsf ftp://data.pdbj.org/pub/pdb/validation_reports/zs/3zsf | HTTPS FTP |
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-Related structure data
Related structure data | 2yjpC 2ylnC 2ieeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 39 - 275 / Label seq-ID: 47 - 283
NCS ensembles :
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-Components
#1: Protein | Mass: 30067.436 Da / Num. of mol.: 8 / 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): PLYSS / References: UniProt: Q5F9M1 #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 19 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 19 TO ALA ...ENGINEERED | Sequence details | N-TERMINAL HIS-TAG CONSTRUCT WITH ENTEROKINA | |
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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: 2.31 Å3/Da / Density % sol: 46.4 % / Description: NONE |
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Crystal grow | pH: 3.5 / Details: 20-30% PEG 3350, 100 MM NA-CITRATE, PH 3.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→48 Å / Num. obs: 81031 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.86 |
Reflection shell | Resolution: 2.32→2.38 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.45 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IEE Resolution: 2.32→48 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / SU B: 16.592 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.275 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.238 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→48 Å
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Refine LS restraints |
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