+Open data
-Basic information
Entry | Database: PDB / ID: 3zui | ||||||
---|---|---|---|---|---|---|---|
Title | OMCI in complex with palmitoleic acid | ||||||
Components | COMPLEMENT INHIBITOR | ||||||
Keywords | IMMUNE SYSTEM / SOFT TICK / ARGASID TICK / C5 / LIPOCALIN COMPLEMENT | ||||||
Function / homology | Calycin beta-barrel core domain / Calycin / Lipocalin / toxin activity / Beta Barrel / extracellular region / Mainly Beta / PALMITOLEIC ACID / Complement inhibitor Function and homology information | ||||||
Biological species | ORNITHODOROS MOUBATA (arthropod) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Roversi, P. / Maillet, I. / Togbe, D. / Couillin, I. / Quesniaux, V.F.J. / Teixeira, M. / Ahmat, N. / Lissina, O. / Boland, W. / Ploss, K. ...Roversi, P. / Maillet, I. / Togbe, D. / Couillin, I. / Quesniaux, V.F.J. / Teixeira, M. / Ahmat, N. / Lissina, O. / Boland, W. / Ploss, K. / Caesar, J.J.E. / Leonhartsberger, S. / Ryffel, B. / Lea, S.M. / Nunn, M.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Bifunctional Lipocalin Ameliorates Murine Immune Complex-Induced Acute Lung Injury. Authors: Roversi, P. / Ryffel, B. / Togbe, D. / Maillet, I. / Teixeira, M. / Ahmat, N. / Paesen, G.C. / Lissina, O. / Boland, W. / Ploss, K. / Caesar, J.J. / Leonhartsberger, S. / Lea, S.M. / Nunn, M.A. #1: Journal: J.Mol.Biol. / Year: 2007 Title: The Structure of Omci, a Novel Lipocalin Inhibitor of the Complement System. Authors: Roversi, P. / Lissina, O. / Johnson, S. / Ahmat, N. / Paesen, G.C. / Ploss, K. / Boland, W. / Nunn, M.A. / Lea, S.M. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3zui.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zui.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/3zui ftp://data.pdbj.org/pub/pdb/validation_reports/zu/3zui | HTTPS FTP |
---|
-Related structure data
Related structure data | 3zuoC 2cm4S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16804.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ORNITHODOROS MOUBATA (arthropod) / Tissue: SALIVARY GLAND / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): WCM105 / References: UniProt: Q5YD59 |
---|---|
#2: Chemical | ChemComp-PAM / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | PALIMITOLE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.7 % / Description: NONE |
---|---|
Crystal grow | pH: 8.5 / Details: 30% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS PH 8.5. |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 24, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→68.4 Å / Num. obs: 15720 / % possible obs: 89.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 22.16 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.71→1.81 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 62.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CM4 Resolution: 1.71→37.26 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.114 Details: REFINEMENT NOTES 1:IDEAL-DIST CONTACT SETUP ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. ALTERNATING CYCLES OF TLS AND REFINEMENT. THE PALMITOLEIC ACID MODELLED IN THE STRUCTURE CONSTITUTES ...Details: REFINEMENT NOTES 1:IDEAL-DIST CONTACT SETUP ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. ALTERNATING CYCLES OF TLS AND REFINEMENT. THE PALMITOLEIC ACID MODELLED IN THE STRUCTURE CONSTITUTES 60 PERCENT OF THE FATTY ACID MIX IN THE SAMPLE AS ANALYSED BY MASS SPECTROMETRY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.37 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.195 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→37.26 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.71→1.83 Å / Total num. of bins used: 8
|