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Yorodumi- PDB-4lih: The crystal structure of Gamma-glutamyl-gamma-aminobutyraldehyde ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lih | ||||||
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Title | The crystal structure of Gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase from Burkholderia cenocepacia J2315 | ||||||
Components | Gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Seattle Structural Genomics Center for Infectious Diseases / NIAID / National Institute of Allergy and Infectious Diseases / SSGCID / aldehyde dehydrogenase | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor Similarity search - Function | ||||||
Biological species | Burkholderia cenocepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: The crystal structure of Gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase from Burkholderia cenocepacia J2315 Authors: Lukacs, C.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lih.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4lih.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 4lih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/4lih ftp://data.pdbj.org/pub/pdb/validation_reports/li/4lih | HTTPS FTP |
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-Related structure data
Related structure data | 4fr8S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 53914.324 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: puuC, BceJ2315_05990, BCAL0603 / Production host: Escherichia coli (E. coli) / References: UniProt: B4E926, aldehyde dehydrogenase (NAD+) #2: Chemical | ChemComp-MES / #3: Chemical | ChemComp-EDO / #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: 2.33 Å3/Da / Density % sol: 47.25 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Morpheus Screen well E2: 0.12 Ethylene glycols, 0.1M buffer 1, 30% ethylene glycol/PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97919 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 332765 / Num. obs: 325553 / % possible obs: 97.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 3.52 / Num. unique all: 23867 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FR8 Resolution: 1.85→48.19 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.075 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.144 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.189 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→48.19 Å
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Refine LS restraints |
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