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- PDB-2vpa: High resolution crystal structure of the antibiotic resistance pr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vpa | |||||||||
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Title | High resolution crystal structure of the antibiotic resistance protein NimA from Deinococcus radiodurans | |||||||||
![]() | NIMA-RELATED PROTEIN | |||||||||
![]() | OXIDOREDUCTASE / COFACTOR / ATOMIC RESOLUTION | |||||||||
Function / homology | ![]() Pyridoxamine 5'-phosphate oxidase-related / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta Similarity search - Domain/homology | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Leiros, H.-K.S. / Tedesco, C. / McSweeney, S.M. | |||||||||
![]() | ![]() Title: High-Resolution Structure of the Antibiotic Resistance Protein Nima from Deinococcus Radiodurans. Authors: Leiros, H.-K.S. / Tedesco, C. / Mcsweeney, S.M. #1: ![]() Title: Structural Basis of 5-Nitroimidazole Antibiotic Resistance: The Crystal Structure of Nima from Deinococcus Radiodurans Authors: Leiros, H.-K.S. / Kozielski-Stuhrmann, S. / Kapp, U. / Terradot, L. / Leonard, G.A. / Mcsweeney, S.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118 KB | Display | ![]() |
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PDB format | ![]() | 90.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1w3oS 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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Unit cell |
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Components
#1: Protein | Mass: 24467.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: INCLUDES THE FIRST 10 RESIDUES OF THE 21 RESIDUE LONG N-TERMINAL HIS TAG Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-PYR / |
#4: Water | ChemComp-HOH / |
Sequence details | THE VECTOR PDEST17 (INVITROGEN) WITH A 21 RESIDUE LONG HIS- TAG (MSYYHHHHHHLESTSLYKKAG) IS ATTACHED ...THE VECTOR PDEST17 (INVITROGEN |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 43.35 % / Description: NONE |
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Crystal grow | Details: 0.6-0.7 M SODIUM ACETATE AND 0.1 M MES PH 6 OR 0.1 M NA CACODYLATE PH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. obs: 65888 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 8.16 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1W3O Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.228 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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