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- PDB-3fve: Crystal structure of diaminopimelate epimerase Mycobacterium tube... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fve | ||||||
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Title | Crystal structure of diaminopimelate epimerase Mycobacterium tuberculosis DapF | ||||||
![]() | Diaminopimelate epimerase | ||||||
![]() | ISOMERASE / alpha/beta / Amino-acid biosynthesis / Lysine biosynthesis | ||||||
Function / homology | ![]() diaminopimelate epimerase / diaminopimelate epimerase activity / lysine biosynthetic process via diaminopimelate / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Usha, V. / Dover, L.G. / Roper, D.I. / Futterer, K. / Besra, G.S. | ||||||
![]() | ![]() Title: Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis Authors: Usha, V. / Dover, L.G. / Roper, D.I. / Futterer, K. / Besra, G.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 | ![]() | 65.5 KB | Display | ![]() |
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PDB format | ![]() | 47.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.4 KB | Display | ![]() |
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Full document | ![]() | 460.2 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bwzS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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2 | ![]()
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Unit cell |
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Details | BIOLOGICAL UNIT IS THE SAME AS ASYM. |
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Components
#1: Protein | Mass: 29864.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P63897, UniProt: P9WP19*PLUS, diaminopimelate epimerase | ||
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#2: Chemical | ChemComp-DTT / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.62 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 9.5 Details: 1.9 M (NH4)H2PO4, 0.1 M bis-tris propane, pH 9.5, 2.5% glycerol, vapor diffusion, temperature 291K, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM Q315r / Detector: CCD / Date: Sep 27, 2008 |
Radiation | Monochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→45.22 Å / Num. all: 14430 / Num. obs: 14430 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Biso Wilson estimate: 64.8 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 |
Reflection shell | Resolution: 2.59→2.73 Å / Redundancy: 13 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2020 / Rsym value: 0.758 / % possible all: 98.4 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1BWZ Resolution: 2.6→45 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.229 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.807 / SU B: 20.884 / SU ML: 0.213 / SU R Cruickshank DPI: 0.416 / SU Rfree: 0.291 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.85 Å2 / Biso mean: 38.103 Å2 / Biso min: 27.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -17.389 Å / Origin y: 73.299 Å / Origin z: -3.47 Å
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