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- PDB-3lwu: Crystal structure of Putative succinylglutamate desuccinylase/asp... -
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Basic information
Entry | Database: PDB / ID: 3lwu | ||||||
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Title | Crystal structure of Putative succinylglutamate desuccinylase/aspartoacylase (YP_749235.1) from Shewanella frigidimarinA NCIMB 400 at 2.10 A resolution | ||||||
![]() | Succinylglutamate desuccinylase/aspartoacylase | ||||||
![]() | HYDROLASE / Putative succinylglutamate desuccinylase/aspartoacylase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Metal-binding / METAL BINDING PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of Putative succinylglutamate desuccinylase/aspartoacylase (YP_749235.1) from Shewanella frigidimarina NCIMB 400 at 2.10 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.1 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.8 KB | Display | ![]() |
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Full document | ![]() | 442.1 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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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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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
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Components
#1: Protein | Mass: 43878.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 10.0000% Glycerol, 12.5000% polyethylene glycol 300, 0.2000M ammonium sulfate, 0.1M phosphate-citrate pH 4.5, 0.006 M zinc chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 7, 2009 / Details: Flat collimating mirror, toroid focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→29.623 Å / Num. obs: 30948 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.815 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 9.47 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ZN HAS BEEN MODELED ON THE BASIS OF ANOMALOUS DIFFERENCE FOURIERS AND ITS USE AS AN ADDITIVE IN THE CRYSTALLIZATION SOLUTION. 5. A SULFATE MOLECULE (SO4) FROM THE CRYSTALLIZATION SOLUTION IS MODELED. 6. AN UNKNOW LIGAND (UNL) HAS BEEN MODELED IN THE ACTIVE SITE NEAR ZN. THE UNL RESEMEBLES A DERIVATIVE OF EITHER SUCCINYL-GLUTAMATE OR GLUTAMATE. 7. RAMACHANDRAN OUTLIER RESIDUE 176 IS WELL SUPPORTED BY THE DENSITY.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.09 Å2 / Biso mean: 21.824 Å2 / Biso min: 9.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.623 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 50.339 Å / Origin y: 22.368 Å / Origin z: 17.512 Å
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