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Yorodumi- PDB-2p7k: Crystal structure of genomically encoded fosfomycin resistance pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p7k | ||||||
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Title | Crystal structure of genomically encoded fosfomycin resistance protein, FosX, from Listeria monocytogenes (hexagonal form) | ||||||
Components | Glyoxalase family protein | ||||||
Keywords | METAL BINDING PROTEIN / hydrolase / FOSFOMYCIN RESISTANCE PROTEIN / MN BINDING / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Fillgrove, K.L. / Pakhomova, S. / Schaab, M. / Newcomer, M.E. / Armstrong, R.N. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Structure and Mechanism of the Genomically Encoded Fosfomycin Resistance Protein, FosX, from Listeria monocytogenes. Authors: Fillgrove, K.L. / Pakhomova, S. / Schaab, M.R. / Newcomer, M.E. / Armstrong, R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p7k.cif.gz | 60 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p7k.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 2p7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p7k_validation.pdf.gz | 392.3 KB | Display | wwPDB validaton report |
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Full document | 2p7k_full_validation.pdf.gz | 401 KB | Display | |
Data in XML | 2p7k_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 2p7k_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/2p7k ftp://data.pdbj.org/pub/pdb/validation_reports/p7/2p7k | HTTPS FTP |
-Related structure data
Related structure data | 2p7lC 2p7mC 2p7oC 2p7pC 2p7qC 1r9cS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 15590.603 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q71YW5, UniProt: Q8Y6I2*PLUS #2: Chemical | #3: 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: 3.7 Å3/Da / Density % sol: 66.71 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 15% PEG 8000, 20 mM Na acetate, 0.1 M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.069 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 13, 2002 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.069 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. all: 6831 / Num. obs: 6831 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rsym value: 0.099 / Net I/σ(I): 6.83 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 666 / Rsym value: 0.44 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R9C Resolution: 3.3→15 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.867 / SU ML: 0.371 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.555 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.3→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.3→3.382 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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