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Yorodumi- PDB-1mwr: Structure of SeMet Penicillin binding protein 2a from methicillin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mwr | ||||||
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Title | Structure of SeMet Penicillin binding protein 2a from methicillin resistant Staphylococcus aureus strain 27r (trigonal form) at 2.45 A resolution. | ||||||
Components | penicillin-binding protein 2a | ||||||
Keywords | BIOSYNTHETIC PROTEIN / penicillin binding protein / beta-lactam / d / d-transpeptidase / d-carboxypeptidase | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase / peptidoglycan L,D-transpeptidase activity / glycosyltransferase activity / penicillin binding / cell wall organization / response to antibiotic / membrane Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å | ||||||
Authors | Lim, D.C. / Strynadka, N.C.J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Structural basis for the beta lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus. Authors: Lim, D. / Strynadka, N.C. | ||||||
History |
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Remark 999 | SEQUENCE At the time of processing, the sequence for this strain was not present in a sequence ... SEQUENCE At the time of processing, the sequence for this strain was not present in a sequence database. However, the protein crystallized contains the engineered mutation Y23M and the first 22 residues were deleted. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mwr.cif.gz | 252.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mwr.ent.gz | 213.2 KB | Display | PDB format |
PDBx/mmJSON format | 1mwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mwr_validation.pdf.gz | 446.9 KB | Display | wwPDB validaton report |
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Full document | 1mwr_full_validation.pdf.gz | 492 KB | Display | |
Data in XML | 1mwr_validation.xml.gz | 47.7 KB | Display | |
Data in CIF | 1mwr_validation.cif.gz | 64.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/1mwr ftp://data.pdbj.org/pub/pdb/validation_reports/mw/1mwr | HTTPS FTP |
-Related structure data
-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
#1: Protein | Mass: 74574.492 Da / Num. of mol.: 2 / Mutation: Y23M, delta 1-22 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 lamda DE3 / References: UniProt: Q93IC2 #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CL / #4: 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: 2.82 Å3/Da / Density % sol: 56.44 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: CdCl2, PEG550MME, HEPES, NaCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2002 |
Radiation | Monochromator: SiO2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 61048 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.044 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.45→2.5 Å / Mean I/σ(I) obs: 2.9 / Num. unique all: 5869 / Rsym value: 0.364 / % possible all: 95.5 |
Reflection | *PLUS Lowest resolution: 25 Å / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 95.5 % / Rmerge(I) obs: 0.364 |
-Processing
Software |
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Refinement | Resolution: 2.45→24.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3363621.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.9299 Å2 / ksol: 0.351871 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→24.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor obs: 0.27 / Rfactor Rfree: 0.323 / Rfactor Rwork: 0.269 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.375 / Rfactor Rwork: 0.319 |