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Yorodumi- PDB-6oad: 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B fr... -
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-Basic information
Entry | Database: PDB / ID: 6oad | ||||||
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Title | 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655. | ||||||
Components | Peptidase B | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Aminopeptidase B | ||||||
Function / homology | Function and homology information 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 | Escherichia coli str. K-12 substr. MG1655 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Wawrzak, Z. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Protein Sci. / Year: 2020 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: Journal: Acta Crystallogr.,Sect.F / Year: 2019 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: Journal: Febs J. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oad.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6oad.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 6oad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oad_validation.pdf.gz | 318.1 KB | Display | wwPDB validaton report |
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Full document | 6oad_full_validation.pdf.gz | 320.6 KB | Display | |
Data in XML | 6oad_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 6oad_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/6oad ftp://data.pdbj.org/pub/pdb/validation_reports/oa/6oad | HTTPS FTP |
-Related structure data
Related structure data | 6ov8C 3ij3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 46502.270 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: pepB, D8B36_06045 / Variant: MG1655 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic References: UniProt: A0A387CSU7, UniProt: P37095*PLUS, PepB aminopeptidase |
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-Non-polymers , 8 types, 3495 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-BCT / #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-PGE / | #8: Chemical | ChemComp-PEG / #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 6.0 mg/ml, 0.01M Tris pH 8.3; Screen: PEGs II (H8), 0.2M Calcium acetate, 0.1M HEPES pH 7.5, 10% (w/v) PEG 8000. Cryo: reservoir + 20% Ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 5, 2019 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 338775 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.054 / Rrim(I) all: 0.112 / Rsym value: 0.098 / Χ2: 1.011 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 16506 / CC1/2: 0.761 / Rpim(I) all: 0.437 / Rrim(I) all: 0.905 / Rsym value: 0.791 / Χ2: 1.007 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IJ3 Resolution: 2.05→29.88 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.004 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.165 / 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: 37.118 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→29.88 Å
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