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Yorodumi- PDB-3gnn: Crystal structure of nicotinate-nucleotide pyrophosphorylase from... -
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-Basic information
Entry | Database: PDB / ID: 3gnn | ||||||
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Title | Crystal structure of nicotinate-nucleotide pyrophosphorylase from Burkholderi pseudomallei | ||||||
Components |
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Keywords | TRANSFERASE / deCODE biostructures / SSGCID / NIAID / SBRI / UWPPG / Glycosyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / NAD biosynthetic process Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei 1710b (bacteria) unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of nicotinate-nucleotide pyrophosphorylase from Burkholderi pseudomallei Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gnn.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gnn.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gnn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gnn_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 3gnn_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | 3gnn_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 3gnn_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/3gnn ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gnn | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31914.139 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria) Strain: 1710b / Gene: nadC, BURPS1710b_1132 / Production host: Escherichia coli (E. coli) References: UniProt: Q3JV59, nicotinate-nucleotide diphosphorylase (carboxylating) #2: Protein/peptide | Mass: 358.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) #3: Water | ChemComp-HOH / | Sequence details | CHAINS D,E ARE ACTUALLY PARTS OF CHAINS A,B. THE AUTHORS COULD NOT DETERMINE THE EXACT SEQUENCE ...CHAINS D,E ARE ACTUALLY PARTS OF CHAINS A,B. THE AUTHORS COULD NOT DETERMINE THE EXACT SEQUENCE FROM THE KNOWN PRIMARY STRUCTURE. THUS THEY WERE MODELED AS UNK IN THIS ENTRY | |
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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: 2.27 Å3/Da / Density % sol: 45.93 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: HAMPTON CRYSTAL SCREEN CONDITION E8, 1.5 M NACL, 10% ETHANOL WITH 25% GLYCEROL AS CRYO-PROTECTANT, 28.7 MG/ML PROTEIN, CRYSTAL ID 109334E8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å |
Detector | Date: Jun 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 27262 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Χ2: 1.151 / Net I/σ(I): 21.998 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.27 / Num. unique all: 2650 / Χ2: 1.134 / % possible all: 97.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→39.14 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.265 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.811 / SU B: 6.813 / SU ML: 0.173 / SU R Cruickshank DPI: 0.303 / SU Rfree: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 100.52 Å2 / Biso mean: 48.358 Å2 / Biso min: 13.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→39.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.311 Å / Total num. of bins used: 20
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