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Yorodumi- PDB-3d0c: Crystal structure of dihydrodipicolinate synthase from Oceanobaci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d0c | ||||||
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Title | Crystal structure of dihydrodipicolinate synthase from Oceanobacillus iheyensis at 1.9 A resolution | ||||||
Components | Dihydrodipicolinate synthase | ||||||
Keywords | LYASE / Lysine biosynthesis / Pyruvate / TIM barrel / NYSGXRC / 9375o / PSI-2 / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity Similarity search - Function | ||||||
Biological species | Oceanobacillus iheyensis HTE831 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Satyanarayana, L. / Eswaramoorthy, S. / Sauder, J.M. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of dihydrodipicolinate synthase from Oceanobacillus iheyensis at 1.9 A resolution. Authors: Satyanarayana, L. / Eswaramoorthy, S. / Sauder, J.M. / 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 | 3d0c.cif.gz | 132.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d0c.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 3d0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/3d0c ftp://data.pdbj.org/pub/pdb/validation_reports/d0/3d0c | 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 THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE. |
-Components
#1: Protein | Mass: 35149.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oceanobacillus iheyensis HTE831 (bacteria) Species: Oceanobacillus iheyensis / Strain: HTE831 / DSM 14371 / JCM 11309 / KCTC 3954 / / Gene: OB2845, DHDPS / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+RIL / References: UniProt: Q8EMJ7, dihydrodipicolinate synthase #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: 2.28 Å3/Da / Density % sol: 45.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Magnesium chloride, 0.1M Lysine, 3% DMSO, 0.1M Tris-HCl pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2008 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 50112 / Num. obs: 50112 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.35 / Num. unique all: 4270 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / 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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Displacement parameters | Biso mean: 27.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016
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