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- PDB-3n6x: Crystal structure of a Putative glutathionylspermidine synthase (... -
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Basic information
Entry | Database: PDB / ID: 3n6x | ||||||
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Title | Crystal structure of a Putative glutathionylspermidine synthase (Mfla_0391) from METHYLOBACILLUS FLAGELLATUS KT at 2.35 A resolution | ||||||
![]() | Putative glutathionylspermidine synthase | ||||||
![]() | LIGASE / Domain of unknown function (DUF404) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | ![]() Dna Ligase; domain 1 - #270 / Rossmann fold - #11290 / Uncharacterised conserved protein UCP005522 / Circularly permuted ATP-grasp type 2 / Circularly permuted ATP-grasp type 2 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of a Putative glutathionylspermidine synthase (Mfla_0391) from METHYLOBACILLUS FLAGELLATUS KT at 2.35 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 | ![]() | 108.9 KB | Display | ![]() |
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PDB format | ![]() | 85.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.7 KB | Display | ![]() |
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Full document | ![]() | 468.5 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 30.6 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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2 | ![]()
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Unit cell |
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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
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Components
#1: Protein | Mass: 53395.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.34 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND . Crystal grow | Temperature: 293 K / pH: 6 | Details: 0.8000M ammonium sulfate, 0.1M MES pH 6.0, Additive: 0.003 M adenosine 5'-triphosphate magnesium salt, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 23, 2010 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR | ||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.35→29.944 Å / Num. obs: 31751 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 43.94 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.98 | ||||||||||||
Reflection shell | Resolution: 2.35→2.43 Å / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.8 / % possible all: 95.8 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: 1. 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 ...Details: 1. 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. 2. GLYCEROL (GOL), SULFLATE (SO4) AND CHLORIDE (CL) MODELED ARE PRESENT PURIFICATION/CRYSTALLIZATION/CRYO CONDITIONS. 3. THE FOLLOWING REGIONS HAVE POOR DENSITY, THE CORRESPONDING MODEL IS NOT RELIABLE: 13-19,33-37,227-231. THE SOLVENT REGION IS NOISY.
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Displacement parameters | Biso mean: 50.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→29.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.43 Å / Total num. of bins used: 16
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