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Yorodumi- PDB-3mae: CRYSTAL STRUCTURE OF PROBABLE DIHYDROLIPOAMIDE ACETYLTRANSFERASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mae | ||||||
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Title | CRYSTAL STRUCTURE OF PROBABLE DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM LISTERIA MONOCYTOGENES 4b F2365 | ||||||
Components | 2-oxoisovalerate dehydrogenase E2 component, dihydrolipoamide acetyltransferase | ||||||
Keywords | TRANSFERASE / 2-oxoacid dehydrogenases acyltransferase / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / Acyltransferase / Lipoyl / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / 2-Layer Sandwich / Alpha Beta / PHOSPHATE ION / : Function and homology information | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Gilmore, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: CRYSTAL STRUCTURE OF A CATALYTIC DOMAIN OF DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM LISTERIA MONOCYTOGENES 4b F2365 Authors: Patskovsky, Y. / Toro, R. / Gilmore, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mae.cif.gz | 149.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mae.ent.gz | 120 KB | Display | PDB format |
PDBx/mmJSON format | 3mae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/3mae ftp://data.pdbj.org/pub/pdb/validation_reports/ma/3mae | HTTPS FTP |
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-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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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 28029.420 Da / Num. of mol.: 3 / Fragment: C-TERMINAL FRAGMENT, RESIDUES 172-416 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: F2365 / Gene: LMOf2365_1391 / Production host: Escherichia coli (E. coli) References: UniProt: Q71ZU8, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-GOL / #5: 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: 3.74 Å3/Da / Density % sol: 67.11 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 100MM SODIUM CITRATE, PH 5.6, 1000MM AMMONIUM DIHYDROGEN PHOSPHATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. obs: 43534 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 3.8 % / Biso Wilson estimate: 48.747 Å2 / Rsym value: 0.148 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0.8 / Rsym value: 0.96 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.124 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.218 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.671 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 1714 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.502→2.566 Å / Total num. of bins used: 20
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