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Yorodumi- PDB-3inn: Crystal structure of pantoate-beta-alanine-ligase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3inn | ||||||
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Title | Crystal structure of pantoate-beta-alanine-ligase in complex with ATP at low occupancy at 2.1 A resolution | ||||||
Components | Pantothenate synthetase | ||||||
Keywords | LIGASE / SSGCID / SBRI / UW / DECODE / NIH / NIAID / BRUCELLA MELITENSIS / PANTOATE BETA ALANINE LIGASE / ATP-binding / Cytoplasm / Nucleotide-binding / Pantothenate biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Brucella melitensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of pantoate-beta-alanine-ligase in complex with ATP at low occupancy at 2.1 A resolution Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Davies, D. / Staker, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3inn.cif.gz | 240.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3inn.ent.gz | 191.8 KB | Display | PDB format |
PDBx/mmJSON format | 3inn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3inn_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3inn_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3inn_validation.xml.gz | 47.7 KB | Display | |
Data in CIF | 3inn_validation.cif.gz | 67.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/3inn ftp://data.pdbj.org/pub/pdb/validation_reports/in/3inn | HTTPS FTP |
-Related structure data
Related structure data | 2ejcS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34834.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: BMEI1593, panC / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8YFC9, pantoate-beta-alanine ligase (AMP-forming) #2: Chemical | #3: Chemical | ChemComp-UNX / #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: 2.18 Å3/Da / Density % sol: 43.67 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9 Details: JCSG+ Screen B3: 20% PEG 6000, 100mM Bicine pH 9.0. Protein at 22 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 72100 / Num. obs: 72100 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 39.63 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 27.31 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2EJC modified with ccp4 program chainsaw Resolution: 2.1→47.95 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.016 / SU ML: 0.136 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.193 / 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: 27.67 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→47.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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