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Yorodumi- PDB-2rca: Crystal structure of the NR3B ligand binding core complex with gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rca | ||||||
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Title | Crystal structure of the NR3B ligand binding core complex with glycine at 1.58 Angstrom resolution | ||||||
Components | Glutamate [NMDA] receptor subunit 3B | ||||||
Keywords | MEMBRANE PROTEIN / Cell junction / Glycoprotein / Ion transport / Ionic channel / Magnesium / Postsynaptic cell membrane / Receptor / Synapse / Transmembrane / Transport | ||||||
Function / homology | Function and homology information glutamate receptor activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / neurotransmitter receptor activity / glycine binding / protein insertion into membrane / regulation of calcium ion transport / cellular response to glycine / monoatomic cation channel activity / presynaptic active zone membrane ...glutamate receptor activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / neurotransmitter receptor activity / glycine binding / protein insertion into membrane / regulation of calcium ion transport / cellular response to glycine / monoatomic cation channel activity / presynaptic active zone membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / calcium ion transmembrane transport / postsynaptic density membrane / modulation of chemical synaptic transmission / neuronal cell body / endoplasmic reticulum membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Yao, Y. / Mayer, M.L. | ||||||
Citation | Journal: Embo J. / Year: 2008 Title: Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors. Authors: Yao, Y. / Harrison, C.B. / Freddolino, P.L. / Schulten, K. / Mayer, M.L. #1: Journal: J.NEUROSCI. / Year: 2006 Title: Characterization of a soluble ligand binding domain of the NMDA receptor regulatory subunit NR3A Authors: Yao, Y. / Mayer, M.L. | ||||||
History |
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Remark 999 | RESIDUES 151 AND 152 GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 561-675 OF THE PROTEIN ...RESIDUES 151 AND 152 GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 561-675 OF THE PROTEIN FROM THE UNP entry Q8VHN2 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rca.cif.gz | 135.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rca.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 2rca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rca_validation.pdf.gz | 462.9 KB | Display | wwPDB validaton report |
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Full document | 2rca_full_validation.pdf.gz | 470.7 KB | Display | |
Data in XML | 2rca_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 2rca_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/2rca ftp://data.pdbj.org/pub/pdb/validation_reports/rc/2rca | HTTPS FTP |
-Related structure data
Related structure data | 2rc7C 2rc8C 2rc9C 2rcbSC 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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2 |
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Unit cell |
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Details | The biological unit is believed to be a dimer of dimers. Molecular packing in the present structure is not biologically relevant. |
-Components
#1: Protein | Mass: 32180.646 Da / Num. of mol.: 2 / Fragment: unp residues 413-560, 676-815 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) Description: Peptides corresponding to A413-R560 and E676-K815 were coupled by a GT dipeptid e synthetic linker Gene: Grin3b / Plasmid: pET22b(+) modified / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMIB (DE3) / References: UniProt: Q8VHN2 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 2.16 Å3/Da / Density % sol: 43.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1 M NaCitrate, 17% PEG 4000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2006 |
Radiation | Monochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→40 Å / Num. all: 76724 / Num. obs: 76724 / % possible obs: 92.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.25 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Pdb entry 2RCB Resolution: 1.58→36.3 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.262 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.97931 / ESU R: 0.107 / ESU R Free: 0.107 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.573 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→36.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.625 Å / Total num. of bins used: 20
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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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