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Yorodumi- PDB-1mwt: Structure of penicillin G acyl-Penicillin binding protein 2a from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mwt | |||||||||
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Title | Structure of penicillin G acyl-Penicillin binding protein 2a from methicillin resistant Staphylococcus aureus strain 27r at 2.45 A resolution. | |||||||||
Components | PBP2a | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / penicillin binding protein / beta-lactam / d / d-transpeptidase / d-carboxypeptidase / penicillin G | |||||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / glycosyltransferase activity / penicillin binding / membrane => GO:0016020 / 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 | 1mwt.cif.gz | 259.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mwt.ent.gz | 215.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/1mwt ftp://data.pdbj.org/pub/pdb/validation_reports/mw/1mwt | HTTPS FTP |
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-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: 73777.250 Da / Num. of mol.: 2 / Fragment: residues 23-668 / Mutation: Y23M, delta 1-22 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mecA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 lamda DE3 References: UniProt: O54286, UniProt: Q93IC2*PLUS, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CL / #4: Chemical | #5: 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: 2.62 Å3/Da / Density % sol: 53.06 % | ||||||||||||||||||||||||||||||||||||||||||
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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→25 Å / Num. all: 56624 / Num. obs: 56624 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.049 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.45→2.5 Å / Mean I/σ(I) obs: 5.3 / Num. unique all: 5401 / Rsym value: 0.207 / % possible all: 94.4 |
Reflection | *PLUS Lowest resolution: 25 Å / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 94.4 % / Rmerge(I) obs: 0.207 |
-Processing
Software |
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Refinement | Resolution: 2.45→24.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2455486.63 / 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: 28.3303 Å2 / ksol: 0.325499 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.1 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: 0.019 / 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: 0.233 / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.234 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.41 / Rfactor Rwork: 0.335 |