[English] 日本語
Yorodumi- PDB-2p7m: Crystal structure of monoclinic form of genomically encoded fosfo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p7m | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of monoclinic form of genomically encoded fosfomycin resistance protein, FosX, from Listeria monocytogenes at pH 6.5 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2p7m.cif.gz | 166.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2p7m.ent.gz | 133.6 KB | Display | PDB format |
PDBx/mmJSON format | 2p7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p7m_validation.pdf.gz | 399.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2p7m_full_validation.pdf.gz | 410.5 KB | Display | |
Data in XML | 2p7m_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 2p7m_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/2p7m ftp://data.pdbj.org/pub/pdb/validation_reports/p7/2p7m | HTTPS FTP |
-Related structure data
Related structure data | 2p7kSC 2p7lC 2p7oC 2p7pC 2p7qC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
2 |
| |||||||||
3 |
| |||||||||
4 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 15590.603 Da / Num. of mol.: 6 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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.73 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18-20% PEG 8000, 0.1M Na citrate, 4-12 mM Na acetate, 10% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2002 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→18.62 Å / Num. all: 68258 / Num. obs: 68258 / % possible obs: 88.4 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.038 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 2336 / Rsym value: 0.457 / % possible all: 60.8 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2P7K Resolution: 1.85→18.62 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.7 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→18.62 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.029
|