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Yorodumi- PDB-3s1y: AMP-C BETA-LACTAMASE (PSEUDOMONAS AERUGINOSA) in complex with a b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s1y | ||||||
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Title | AMP-C BETA-LACTAMASE (PSEUDOMONAS AERUGINOSA) in complex with a beta-lactamase inhibitor | ||||||
Components | Beta-lactamase | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Hydrolase / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å | ||||||
Authors | Scapin, G. / Lu, J. / Fitzgerald, P.M.D. / Sharma, N. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Side chain SAR of bicyclic Beta-lactamase inhibitors (BLIs). 2. N-Alkylated and open chain analogs of MK-8712 Authors: Chen, H. / Blizzard, T.A. / Kim, S. / Wu, J. / Young, K. / Park, Y.W. / Ogawa, A.M. / Raghoobar, S. / Painter, R.E. / Wisniewski, D. / Hairston, N. / Fitzgerald, P. / Sharma, N. / Scapin, G. ...Authors: Chen, H. / Blizzard, T.A. / Kim, S. / Wu, J. / Young, K. / Park, Y.W. / Ogawa, A.M. / Raghoobar, S. / Painter, R.E. / Wisniewski, D. / Hairston, N. / Fitzgerald, P. / Sharma, N. / Scapin, G. / Lu, J. / Hermes, J. / Hammond, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s1y.cif.gz | 163 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s1y.ent.gz | 132.9 KB | Display | PDB format |
PDBx/mmJSON format | 3s1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/3s1y ftp://data.pdbj.org/pub/pdb/validation_reports/s1/3s1y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40637.848 Da / Num. of mol.: 1 / Mutation: R397A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ampC, PA4110 / Plasmid: pET 26 / Production host: Escherichia coli (E. coli) / References: UniProt: P24735, beta-lactamase | ||||
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#2: Chemical | ChemComp-S1Y / [( | ||||
#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | THE STARTING MATERIAL IS A CLOSED RING BETA-LACTAMASE INHIBITOR, THAT REACTS WITH SER90 TO BECOME ...THE STARTING MATERIAL IS A CLOSED RING BETA-LACTAMASE INHIBITOR, THAT REACTS WITH SER90 TO BECOME THE OPEN RING COMPOUND, S1Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% PEG 3350, 10% 2-propanol, 100 mM Imidazole, microseeding, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 2, 2007 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→99 Å / Num. all: 75040 / Num. obs: 74960 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.35→1.43 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1 / Num. unique all: 12346 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.392 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R Free: 0.072 / 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: 11.657 Å2
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Refine analyze | Luzzati coordinate error obs: 0.196 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.435 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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