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Open data
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Basic information
Entry | Database: PDB / ID: 1bwz | ||||||
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Title | DIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE | ||||||
![]() | PROTEIN (DIAMINOPIMELATE EPIMERASE) | ||||||
![]() | ISOMERASE / METABOLIC ROLE / STRUCTURAL CLASSIFICATION | ||||||
Function / homology | ![]() diaminopimelate epimerase / diaminopimelate epimerase activity / lysine biosynthetic process via diaminopimelate / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cirilli, M. / Zheng, R. / Scapin, G. / Blanchard, J.S. | ||||||
![]() | ![]() Title: Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase. Authors: Cirilli, M. / Zheng, R. / Scapin, G. / Blanchard, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.3 KB | Display | ![]() |
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PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423 KB | Display | ![]() |
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Full document | ![]() | 431.9 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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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
#1: Protein | Mass: 30295.584 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 62 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion, hanging drop / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→23.79 Å / Num. obs: 9691 / % possible obs: 89.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.061 / Net I/σ(I): 11.61 |
Reflection shell | Resolution: 2.72→2.83 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 10.89 / Rsym value: 0.061 / % possible all: 51.6 |
Reflection | *PLUS Num. measured all: 33313 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 51.6 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 6.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 37.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→23.79 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARAM19X.PR / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 7 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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