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Yorodumi- PDB-1mns: ON THE ROLE OF LYSINE 166 IN THE MECHANISM OF MANDELATE RACEMASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mns | |||||||||
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Title | ON THE ROLE OF LYSINE 166 IN THE MECHANISM OF MANDELATE RACEMASE FROM PSEUDOMONAS PUTIDA: MECHANISTIC AND CRYSTALLOGRAPHIC EVIDENCE FOR STEREOSPECIFIC ALKYLATION BY (R)-ALPHA-PHENYLGLYCIDATE | |||||||||
Components | MANDELATE RACEMASE | |||||||||
Keywords | RACEMASE | |||||||||
Function / homology | Function and homology information mandelate racemase / mandelate racemase activity / mandelate catabolic process / amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Pseudomonas putida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Neidhart, D.J. / Landro, J.A. / Kozarich, J.W. | |||||||||
Citation | Journal: Biochemistry / Year: 1994 Title: The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate. Authors: Landro, J.A. / Gerlt, J.A. / Kozarich, J.W. / Koo, C.W. / Shah, V.J. / Kenyon, G.L. / Neidhart, D.J. / Fujita, S. / Petsko, G.A. #1: Journal: Biochemistry / Year: 1991 Title: Mechanism of the Reaction Catalyzed by Mandelate Racemase 2. Crystal Structure of Mandelate Racemase at 2.5 Angstroms Resolution: Identification of the Active Site and Possible Catalytic Residues Authors: Neidhart, D.J. / Howell, P.L. / Petsko, G.A. / Powers, V.M. / Li, R. / Kenyon, G.L. / Gerlt, J.A. #2: Journal: Nature / Year: 1990 Title: Mandelate Racemase and Muconate Lactonizing Enzyme are Mechanistically Distinct and Structurally Homologous Authors: Neidhart, D.J. / Kenyon, G.L. / Gerlt, J.A. / Petsko, G.A. #3: Journal: To be Published Title: Refined High-Resolution X-Ray Structures of Mandelate Racemase in Complex with Catalytically Active Metal Ions Authors: Neidhart, D.J. | |||||||||
History |
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Remark 700 | SHEET BETA SHEETS ARE NAMED FOR THE MAJOR DOMAINS IN WHICH THEY OCCUR: "N" FOR N-TERMINAL DOMAIN, ...SHEET BETA SHEETS ARE NAMED FOR THE MAJOR DOMAINS IN WHICH THEY OCCUR: "N" FOR N-TERMINAL DOMAIN, "B" FOR BETA-BARREL DOMAIN, AND "C" FOR C-TERMINAL DOMAIN. "F" REFERS TO THE ACTIVE SITE FLAP. LIKEWISE, ALPHA HELICES ARE NAMED WITH TWO CHARACTERS, THE FIRST REFERRING TO THE DOMAIN IN WHICH THEY OCCUR. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mns.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mns.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/1mns ftp://data.pdbj.org/pub/pdb/validation_reports/mn/1mns | HTTPS FTP |
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-Related structure data
-Links
-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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-Components
#1: Protein | Mass: 38384.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / References: UniProt: P11444, mandelate racemase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-APG / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | MANDELATE RACEMASE IS MOST ACTIVE WITH A MAGNESIUM (II) ION BOUND IN THE ACTIVE SITE. IN THIS ...MANDELATE RACEMASE IS MOST ACTIVE WITH A MAGNESIUM (II) ION BOUND IN THE ACTIVE SITE. IN THIS CRYSTAL STRUCTURE OF MANDELATE RACEMASE INACTIVATE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.19 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging dropDetails: taken from Neidhart, D.J. et al (1991). Biochemistry, 30, 9264-9273. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2 Å / % possible obs: 83 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Num. measured all: 62094 / Rmerge(I) obs: 0.075 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.153 / Rfactor obs: 0.153 / Highest resolution: 2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection obs: 22159 / σ(I): 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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