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Yorodumi- PDB-1nxe: A Novel NADH Allosteric Regulator Site is Found on the Surface of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nxe | ||||||
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Title | A Novel NADH Allosteric Regulator Site is Found on the Surface of the Hexameric Type II Phe383Ala Variant of Citrate Synthase | ||||||
Components | Citrate synthase | ||||||
Keywords | TRANSFERASE / citrate synthase / NADH / allosteric | ||||||
Function / homology | Function and homology information citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / NADH binding / protein hexamerization / tricarboxylic acid cycle / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Maurus, R. / Nguyen, N.T. / Stokell, D.J. / Ayed, A. / Hultin, P.G. / Duckworth, H.W. / Brayer, G.D. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Insights into the evolution of allosteric properties. The NADH binding site of hexameric type II citrate synthases. Authors: Maurus, R. / Nguyen, N.T. / Stokell, D.J. / Ayed, A. / Hultin, P.G. / Duckworth, H.W. / Brayer, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nxe.cif.gz | 192.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nxe.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nxe_validation.pdf.gz | 393.1 KB | Display | wwPDB validaton report |
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Full document | 1nxe_full_validation.pdf.gz | 434.8 KB | Display | |
Data in XML | 1nxe_validation.xml.gz | 24 KB | Display | |
Data in CIF | 1nxe_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/1nxe ftp://data.pdbj.org/pub/pdb/validation_reports/nx/1nxe | HTTPS FTP |
-Related structure data
Related structure data | 1nxgC 1k3p 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: 48048.902 Da / Num. of mol.: 2 / Mutation: F383A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GLTA OR GLUT OR ICDB OR B0720 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABH7, citrate (Si)-synthase #2: Chemical | ChemComp-SO4 / #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: 4.31 Å3/Da / Density % sol: 71.44 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Date: Feb 7, 2002 |
Radiation | Monochromator: mirrors / 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. obs: 54292 / Observed criterion σ(I): 0 |
Reflection | *PLUS Lowest resolution: 50 Å / Redundancy: 3.8 % / Num. measured all: 485765 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.34 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 8.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K3P 1k3p Resolution: 2.3→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refinement | *PLUS Lowest resolution: 10 Å / Rfactor obs: 0.17 / Rfactor Rwork: 0.17 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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