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Yorodumi- PDB-3guz: Structural and substrate-binding studies of pantothenate synthena... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3guz | ||||||
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Title | Structural and substrate-binding studies of pantothenate synthenate (PS)provide insights into homotropic inhibition by pantoate in PS's | ||||||
Components | Pantothenate synthetase | ||||||
Keywords | LIGASE / Pantothenate biosynthesis / substrate binding / competitive inhibition / Rossmann fold / non-canonical pantoate binding-site / ATP-binding / Cytoplasm / Nucleotide-binding | ||||||
Function / homology | Function and homology information pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / protein homodimerization activity / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Chakrabarti, K.S. / Thakur, K.G. / Gopal, B. / Sarma, S.P. | ||||||
Citation | Journal: Febs J. / Year: 2010 Title: X-ray crystallographic and NMR studies of pantothenate synthetase provide insights into the mechanism of homotropic inhibition by pantoate Authors: Chakrabarti, K.S. / Thakur, K.G. / Gopal, B. / Sarma, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3guz.cif.gz | 149.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3guz.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 3guz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3guz_validation.pdf.gz | 455.3 KB | Display | wwPDB validaton report |
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Full document | 3guz_full_validation.pdf.gz | 459.6 KB | Display | |
Data in XML | 3guz_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 3guz_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/3guz ftp://data.pdbj.org/pub/pdb/validation_reports/gu/3guz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19859.182 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: V52A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: panC / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) References: UniProt: P31663, pantoate-beta-alanine ligase (AMP-forming) #2: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 10% PEG 4000, 100mM NaCl, 100mM acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 10, 2009 / Details: HELIOS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→34.78 Å / Num. obs: 43231 / % possible obs: 96.2 % / Redundancy: 2.5 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2 / Num. unique all: 5676 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→30.56 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.45 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.112 / 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: 11.614 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→30.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.669→1.713 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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