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Yorodumi- PDB-3ilv: Crystal structure of a glutamine-dependent NAD(+) synthetase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ilv | ||||||
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Title | Crystal structure of a glutamine-dependent NAD(+) synthetase from Cytophaga hutchinsonii | ||||||
Components | Glutamine-dependent NAD(+) synthetase | ||||||
Keywords | LIGASE / NAD(+) synthetase / Cytophaga hutchinsonii / Protein Structure Initiative II(PSI II) / NYSGXRC / 11244e / Structural Genomics / New York SGX Research Center for Structural Genomics / ATP-binding / NAD / Nucleotide-binding | ||||||
Function / homology | Function and homology information NAD+ synthase (glutamine-hydrolysing) / NAD+ synthase (glutamine-hydrolyzing) activity Similarity search - Function | ||||||
Biological species | Cytophaga hutchinsonii ATCC 33406 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å | ||||||
Authors | Palani, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a glutamine-dependent NAD(+) synthetase from Cytophaga hutchinsonii Authors: Palani, K. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ilv.cif.gz | 129.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ilv.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ilv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ilv_validation.pdf.gz | 429.3 KB | Display | wwPDB validaton report |
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Full document | 3ilv_full_validation.pdf.gz | 444.1 KB | Display | |
Data in XML | 3ilv_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 3ilv_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/3ilv ftp://data.pdbj.org/pub/pdb/validation_reports/il/3ilv | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 72604.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cytophaga hutchinsonii ATCC 33406 (bacteria) Strain: ATCC 33406/NCIMB 9469 / Gene: CHU-2417, CHU_2417 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q11SE1, UniProt: A0A6N4STA8*PLUS, NAD+ synthase (glutamine-hydrolysing) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Sodium acetate trihydrate, 2.0M Sodium formate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2009 / Details: MIRRORS |
Radiation | Monochromator: Si(III) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→39.74 Å / Num. all: 61220 / Num. obs: 57695 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.5 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.79→39.74 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 148707.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.413 Å2 / ksol: 0.34815 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.79→39.74 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.79→1.9 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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