+Open data
-Basic information
Entry | Database: PDB / ID: 1bwz | ||||||
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Title | DIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE | ||||||
Components | PROTEIN (DIAMINOPIMELATE EPIMERASE) | ||||||
Keywords | ISOMERASE / METABOLIC ROLE / STRUCTURAL CLASSIFICATION | ||||||
Function / homology | Function and homology information diaminopimelate epimerase / diaminopimelate epimerase activity / lysine biosynthetic process via diaminopimelate / cytosol Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.72 Å | ||||||
Authors | Cirilli, M. / Zheng, R. / Scapin, G. / Blanchard, J.S. | ||||||
Citation | Journal: Biochemistry / Year: 1998 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bwz.cif.gz | 59.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bwz.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bwz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/1bwz ftp://data.pdbj.org/pub/pdb/validation_reports/bw/1bwz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-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.) Haemophilus influenzae (bacteria) / Gene: DAPF / Plasmid: PET 23A(+) / Species (production host): Escherichia coli / Gene (production host): DAPF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P44859, diaminopimelate epimerase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.72→23.79 Å / Cross valid method: THROUGHOUT / σ(F): 2
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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: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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