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Yorodumi- PDB-3eb2: Crystal structure of Dihydrodipicolinate Synthase from Rhodopseud... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eb2 | ||||||
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Title | Crystal structure of Dihydrodipicolinate Synthase from Rhodopseudomonas palustris at 2.0A resolution | ||||||
Components | Putative dihydrodipicolinate synthetase | ||||||
Keywords | LYASE / LYSINE BIOSYNTHESIS / PYRUVATE / TIM BARREL / NYSGXRC / 11102O / PSI2. / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å | ||||||
Authors | Satyanarayana, L. / 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 Dihydrodipicolinate Synthase from Rhodopseudomonas palustris at 2.0A resolution Authors: Satyanarayana, L. / 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 | 3eb2.cif.gz | 233.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eb2.ent.gz | 188 KB | Display | PDB format |
PDBx/mmJSON format | 3eb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eb2_validation.pdf.gz | 466.1 KB | Display | wwPDB validaton report |
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Full document | 3eb2_full_validation.pdf.gz | 486 KB | Display | |
Data in XML | 3eb2_validation.xml.gz | 48.8 KB | Display | |
Data in CIF | 3eb2_validation.cif.gz | 69.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/3eb2 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/3eb2 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
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: 32508.338 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Top10-Invitrogen Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: palustris / Gene: dapA1, RPA1571 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon+RIL / References: UniProt: Q6N9H8, dihydrodipicolinate synthase #2: Chemical | #3: 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: 2.5 Å3/Da / Density % sol: 50.85 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 1,500, 0.1M Bis-Tris pH 5.5, 0.025M Trimethylamine hydrochloride., VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 10, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. all: 82938 / Num. obs: 82938 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.04→2.11 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 11.1 / Num. unique all: 7055 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.04→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.04→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.17 Å / Rfactor Rfree error: 0.013
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