+Open data
-Basic information
Entry | Database: PDB / ID: 1xs0 | ||||||
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Title | Structure of the E. coli Ivy protein | ||||||
Components | Inhibitor of vertebrate lysozyme | ||||||
Keywords | HYDROLASE INHIBITOR / alpha beta fold / dimer | ||||||
Function / homology | Function and homology information lysozyme inhibitor activity / negative regulation of catalytic activity / chaperone-mediated protein folding / outer membrane-bounded periplasmic space / periplasmic space / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.58 Å | ||||||
Authors | Abergel, C. / Monchois, V. / Byrn, D. / Lazzaroni, J.C. / Claverie, J.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: Structure and evolution of the Ivy protein family, unexpected lysozyme inhibitors in Gram-negative bacteria. Authors: Abergel, C. / Monchois, V. / Byrne, D. / Chenivesse, S. / Lembo, F. / Lazzaroni, J.C. / Claverie, J.M. #1: Journal: J.Biol.Chem. / Year: 2001 Title: Escherichia coli ykfE ORFan gene encodes a potent inhibitor of C-type lysozyme Authors: Monchois, V. / Abergel, C. / Sturgis, J. / Jeudy, S. / Claverie, J.M. #2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2000 Title: Crystallization and preliminary crystallographic study of b0220, an 'ORFan' protein of unknown function from Escherichia coli Authors: Abergel, C. / Monchois, V. / Chenivesse, S. / Jeudy, S. / Claverie, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xs0.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xs0.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 1xs0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xs0_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 1xs0_full_validation.pdf.gz | 468.1 KB | Display | |
Data in XML | 1xs0_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 1xs0_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/1xs0 ftp://data.pdbj.org/pub/pdb/validation_reports/xs/1xs0 | HTTPS FTP |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15060.833 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P45502, UniProt: P0AD59*PLUS #2: 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: 1.99 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: 1.4M sodium citrate, 8% PEG 8000, 20mM TRIS, 50mM NaCl, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 105 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97917, 0.97941, 0.97393 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 30, 2000 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.58→40.7 Å / Num. all: 44577 / Num. obs: 44577 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 9.3 / Redundancy: 3 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.037 | ||||||||||||
Reflection shell | Resolution: 1.58→1.67 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 3539 / Rsym value: 0.223 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.58→14.52 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 823714.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.5474 Å2 / ksol: 0.390667 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.58→14.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.68 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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