+Open data
-Basic information
Entry | Database: PDB / ID: 1gpq | ||||||
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Title | Structure of ivy complexed with its target, HEWL | ||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / LYSOZYME-INHIBITOR COMPLEX / TYPE-C LYSOZYME INHIBITOR / HYDROLASE / GLYCOSIDASE / BACTERIAL TARGETS AT IGS-CNRS / FRANCE / BIGS / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information lysozyme inhibitor activity / negative regulation of catalytic activity / chaperone-mediated protein folding / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...lysozyme inhibitor activity / negative regulation of catalytic activity / chaperone-mediated protein folding / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / outer membrane-bounded periplasmic space / defense response to Gram-negative bacterium / killing of cells of another organism / periplasmic space / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / protein homodimerization activity / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Abergel, C. / Monchois, V. / 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. / Claverie, J. #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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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gpq.cif.gz | 124.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gpq.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 1gpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gpq_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
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Full document | 1gpq_full_validation.pdf.gz | 449.2 KB | Display | |
Data in XML | 1gpq_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 1gpq_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/1gpq ftp://data.pdbj.org/pub/pdb/validation_reports/gp/1gpq | HTTPS FTP |
-Related structure data
Related structure data | 1uuzC 1xs0C 1helS 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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Unit cell |
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-Components
#1: Protein | Mass: 14973.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH HEWL IN CRYSTAL / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P45502, UniProt: P0AD59*PLUS #2: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: COMPLEXED WITH IVY IN CRYSTAL / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P00698, lysozyme #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38 % Description: UNCOMPLEXED, AND UNREFINED MAD IVY STRUCTURE WAS ALSO USED FOR MOLECULAR REPLACEMENT |
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Crystal grow | pH: 9 Details: 15% PEG 4000, 5% GLYCEROL, CHES BUFFER 0.1M PH 9.0, PROTEIN CONCENTRATION: 5MG.ML-1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798 |
Detector | Date: Aug 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. obs: 58982 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 4.1 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HEL Resolution: 1.6→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 688920.93 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.18 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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