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Yorodumi- PDB-2iwd: Oxacilloyl-acylated MecR1 extracellular antibiotic-sensor domain. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iwd | |||||||||
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Title | Oxacilloyl-acylated MecR1 extracellular antibiotic-sensor domain. | |||||||||
Components | Methicillin resistance mecR1 protein | |||||||||
Keywords | ANTIBIOTIC RESISTANCE / BACTERIAL ANTIBIOTIC RESISTANCE / OXACILLIN / BETA-LACTAMASE / MRSA / METHICILLIN RESISTANCE / BETA-LACTAMIC ANTIBIOTICS / PENICILLIN-BINDING PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Marrero, A. / Mallorqui-Fernandez, G. / Guevara, T. / Garcia-Castellanos, R. / Gomis-Ruth, F.X. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Unbound and Acylated Structures of the Mecr1 Extracellular Antibiotic-Sensor Domain Provide Insights Into the Signal-Transduction System that Triggers Methicillin Resistance. Authors: Marrero, A. / Mallorqui-Fernandez, G. / Guevara, T. / Garcia-Castellanos, R. / Gomis-Ruth, F.X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iwd.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iwd.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 2iwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iwd_validation.pdf.gz | 459.9 KB | Display | wwPDB validaton report |
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Full document | 2iwd_full_validation.pdf.gz | 463 KB | Display | |
Data in XML | 2iwd_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 2iwd_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/2iwd ftp://data.pdbj.org/pub/pdb/validation_reports/iw/2iwd | HTTPS FTP |
-Related structure data
Related structure data | 2iwbC 2iwcSC C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 29250.361 Da / Num. of mol.: 1 Fragment: EXTRACELLULAR PENICILLIN-SENSOR DOMAIN, RESIDUES 340-585 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Plasmid: PET28A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P0A0B0 |
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#2: Chemical | ChemComp-1S6 / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.1 % |
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Crystal grow | pH: 6.5 / Details: 1.8M TRIBASIC AMMONIUM CITRATE AT PH6.5, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.6 Å / Num. obs: 10438 / % possible obs: 99.5 % / Observed criterion σ(I): 1.5 / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 4.6 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IWC Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 18.826 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.562 / ESU R Free: 0.278 / 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: 44.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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