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Yorodumi- PDB-3hum: Crystal structure of Penicillin binding protein 4 from Staphyloco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hum | ||||||
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Title | Crystal structure of Penicillin binding protein 4 from Staphylococcus aureus COL in complex with Cefotaxime | ||||||
Components | Penicillin-binding protein 4 | ||||||
Keywords | HYDROLASE/Antibiotics / Penicillin binding protein 4 / Cefotaxime / beta-lactamase / Serine type D-Ala / D-Ala-carboxypeptidase / Antibiotics / HYDROLASE-Antibiotics complex | ||||||
Function / homology | Function and homology information serine-type D-Ala-D-Ala carboxypeptidase activity / beta-lactam antibiotic catabolic process / peptidoglycan biosynthetic process / cell wall organization / beta-lactamase activity / regulation of cell shape / membrane => GO:0016020 / response to antibiotic / proteolysis / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Navratna, V. / Gopal, B. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2009 Title: Molecular basis for the role of Staphylococcus aureus Penicillin Binding Protein 4 in antimicrobial resistance Authors: Navratna, V. / Nadig, S. / Sood, V. / Prasad, K. / Arakere, G. / Gopal, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hum.cif.gz | 158.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hum.ent.gz | 121.9 KB | Display | PDB format |
PDBx/mmJSON format | 3hum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hum_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3hum_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3hum_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 3hum_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/3hum ftp://data.pdbj.org/pub/pdb/validation_reports/hu/3hum | HTTPS FTP |
-Related structure data
Related structure data | 3hunC 1tvfS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 50678.930 Da / Num. of mol.: 2 / Mutation: T189S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: pbp4 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 References: UniProt: Q5HI26, UniProt: A0A0H2WY27*PLUS, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THERE ARE CONFLICT BETWEEN SEQRES (SER A,B 189) AND SEQUENCE DATABASE (THR, 189). THE AUTHOR ...THERE ARE CONFLICT BETWEEN SEQRES (SER A,B 189) AND SEQUENCE DATABASE (THR, 189). THE AUTHOR BELIEVE THAT THE SEQRES IS CORRECT AND IS THE TRUE IDENTITY OF THESE RESIDUES AND IS NATURAL MUTANT. | |
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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: 2.11 Å3/Da / Density % sol: 41.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 24% PEG3350, 240mM Ammonium Sulphate, 100mM Bis-tris, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9791 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 3, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.34 Å / Num. obs: 38899 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 7 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4 / Num. unique all: 36895 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TVF Resolution: 2.3→39.34 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.86 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.247 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.802 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→39.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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