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- PDB-6ov8: 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ov8 | ||||||
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Title | 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655 | ||||||
![]() | Peptidase B | ||||||
![]() | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Aminopeptidase B | ||||||
Function / homology | ![]() PepB aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / peptidase activity / manganese ion binding / proteolysis / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Shuvalova, L. / Wawrzak, Z. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis. Authors: Minasov, G. / Lam, M.R. / Rosas-Lemus, M. / Slawek, J. / Woinska, M. / Shabalin, I.G. / Shuvalova, L. / Palsson, B.O. / Godzik, A. / Minor, W. / Satchell, K.J.F. #1: ![]() Title: Structural comparison of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida with PobA from other Pseudomonas spp. and other monooxygenases. Authors: Lazar, J.T. / Shuvalova, L. / Rosas-Lemus, M. / Kiryukhina, O. / Satchell, K.J.F. / Minasov, G. #2: ![]() Title: Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain. Authors: Shabalin, I.G. / Gritsunov, A. / Hou, J. / Slawek, J. / Miks, C.D. / Cooper, D.R. / Minor, W. / Christendat, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 967.8 KB | Display | ![]() |
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PDB format | ![]() | 809.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 88.5 KB | Display | |
Data in CIF | ![]() | 124.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oadSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46924.324 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: pepB, yfhI, b2523, JW2507 / Variant: MG1655 / Plasmid: pMCSG53 / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.96 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 8.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 1mM Zn, 1mM Mn Screen: Classics II (F10), 0.2M Sodium chloride, 0.1M BIS-TRIS pH 5.5, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2019 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 85965 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.059 / Rrim(I) all: 0.149 / Rsym value: 0.136 / Χ2: 1.19 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4231 / CC1/2: 0.837 / Rpim(I) all: 0.341 / Rrim(I) all: 0.861 / Rsym value: 0.79 / Χ2: 1.001 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6OAD Resolution: 2.61→29.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.908 / SU B: 22.881 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 2.558 / ESU R Free: 0.314 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.039 Å2
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Refinement step | Cycle: 1 / Resolution: 2.61→29.76 Å
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Refine LS restraints |
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