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Yorodumi- PDB-3e5d: Crystal structure of a putative glyoxalase i (lmof2365_0426) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e5d | ||||||
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Title | Crystal structure of a putative glyoxalase i (lmof2365_0426) from listeria monocytogenes str. 4b f2365 at 2.70 A resolution | ||||||
Components | Putative Glyoxalase ILactoylglutathione lyase | ||||||
Keywords | LYASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Roll / Alpha Beta / Unknown ligand / : Function and homology information | ||||||
Biological species | Listeria monocytogenes str. 4b F2365 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Putative Glyoxalase I (YP_013033.1) from LISTERIA MONOCYTOGENES 4b F2365 at 2.70 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e5d.cif.gz | 35.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e5d.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 3e5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/3e5d ftp://data.pdbj.org/pub/pdb/validation_reports/e5/3e5d | 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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Details | AUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS THAT FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS. |
-Components
#1: Protein | Mass: 14502.468 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes str. 4b F2365 (bacteria) Gene: LMOf2365_0426 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q723Q1 |
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#2: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.42 Å3/Da / Density % sol: 77.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.1M sodium citrate, 0.15M sodium chloride, 0.1M TRIS pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 27, 2008 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→29.136 Å / Num. obs: 8775 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 103.91 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→29.136 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 13.998 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.189 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 RECORD CONTAINS 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. AN UNKNOWN LIGAND (UNL) HAS BEEN TENTATIVELY MODELED AT WHAT APPEARS TO BE THE PUTATIVE ACTIVE SITE(S) SURROUNDED BY RESIDUES HIS5, PHE39, GLU53, ARG57, HIS73, ASP107, GLU111 AND GLU123.
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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: 57.474 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.136 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.701→2.771 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 59.8985 Å / Origin y: 22.1081 Å / Origin z: 31.8695 Å
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