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Yorodumi- PDB-2poz: Crystal structure of a putative dehydratase from Mesorhizobium loti -
+Open data
-Basic information
Entry | Database: PDB / ID: 2poz | ||||||
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Title | Crystal structure of a putative dehydratase from Mesorhizobium loti | ||||||
Components | Putative dehydratase | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / 9283a / putative dehydratase / octamer / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal ...Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Mesorhizobium loti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å | ||||||
Authors | Sugadev, R. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative dehydratase from Mesorhizobium loti. Authors: Sugadev, R. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2poz.cif.gz | 573.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2poz.ent.gz | 492.1 KB | Display | PDB format |
PDBx/mmJSON format | 2poz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/2poz ftp://data.pdbj.org/pub/pdb/validation_reports/po/2poz | 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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-Components
#1: Protein | Mass: 43444.055 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mll9372 / Plasmid: pSGX3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q981H6 #2: 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: 2.43 Å3/Da / Density % sol: 49.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 0.2M Ammonium acetate, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2007 / Details: Mirrors |
Radiation | Monochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. all: 200694 / Num. obs: 200694 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.04→2.11 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 1 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.04→42.94 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 61410.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.2981 Å2 / ksol: 0.360403 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.04→42.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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