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- PDB-2hmc: The Crystal Structure of Dihydrodipicolinate Synthase DapA from A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hmc | ||||||
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Title | The Crystal Structure of Dihydrodipicolinate Synthase DapA from Agrobacterium tumefaciens | ||||||
![]() | Dihydrodipicolinate synthase | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta Barrel (TIM barrel) / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y. / Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The Crystal Structure of Dihydrodipicolinate Synthase DapA from Agrobacterium tumefaciens Authors: Kim, Y. / Zhang, R. / Xu, X. / Zheng, H. / Edwards, A. / Savchenko, A. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.1 KB | Display | ![]() |
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PDB format | ![]() | 66.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.9 KB | Display | ![]() |
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Full document | ![]() | 436.3 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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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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Details | hexamer the asymmetric unit contains a monomer and the others are generated by -x+y, y,-z+1/2 y,1-x+y,z+1/2 1-x+y,1-x,z -x,1-x+y,-z 1+y,1+x,-z |
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Components
#1: Protein | Mass: 37639.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Agrobacterium tumefaciens / Strain: C58 / Gene: dapA / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.2M Tri-Lithium Citrate, 20% PEG3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-3 / Detector: CCD / Date: Jun 22, 2006 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→31.92 Å / Num. all: 29275 / Num. obs: 29211 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 25.6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 18.6 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1404 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.017 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→31.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 4.0667 Å / Origin y: 34.1192 Å / Origin z: 12.2766 Å
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