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Yorodumi- PDB-5z2p: ThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketogl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z2p | ||||||
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Title | ThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketoglutarate for 5 min | ||||||
Components | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | ||||||
Keywords | TRANSFERASE / complex | ||||||
Function / homology | Function and homology information 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity / menaquinone biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / magnesium ion binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Qin, M.M. / Guo, Z.H. | ||||||
Funding support | Hong Kong, 1items
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Citation | Journal: Biochem. J. / Year: 2018 Title: Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis. Authors: Qin, M.M. / Song, H.G. / Dai, X. / Chen, Y.Z. / Guo, Z.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z2p.cif.gz | 897.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z2p.ent.gz | 736.1 KB | Display | PDB format |
PDBx/mmJSON format | 5z2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/5z2p ftp://data.pdbj.org/pub/pdb/validation_reports/z2/5z2p | HTTPS FTP |
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-Related structure data
Related structure data | 5ejmC 5z2rC 5z2uC 5ej8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 61405.766 Da / Num. of mol.: 8 / Mutation: R413K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: menD, b2264, JW5374 / Variant: 1 / Production host: Escherichia coli (E. coli) References: UniProt: P17109, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase |
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-Non-polymers , 5 types, 2557 molecules
#2: Chemical | ChemComp-TD6 / ( #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-FMT / #5: Chemical | #6: 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: 2.41 Å3/Da / Density % sol: 48.91 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.14M Magnesium formate, 12% PEG 3350, 0.1M HEPES PH 7.5 PH range: 7.2-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20.64 Å / Num. obs: 159070 / % possible obs: 78.1 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 2 % / Rmerge(I) obs: 0.127 / % possible all: 77.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EJ8 Resolution: 2.3→20.64 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 18.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.02 Å2 / Biso mean: 16.72 Å2 / Biso min: 4.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→20.64 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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