+Open data
-Basic information
Entry | Database: PDB / ID: 3zuo | ||||||
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Title | OMCI in complex with leukotriene B4 | ||||||
Components | COMPLEMENT INHIBITOR | ||||||
Keywords | IMMUNE SYSTEM | ||||||
Function / homology | Calycin beta-barrel core domain / Calycin / Lipocalin / toxin activity / Beta Barrel / extracellular region / Mainly Beta / LEUKOTRIENE B4 / Complement inhibitor Function and homology information | ||||||
Biological species | ORNITHODOROS MOUBATA (arthropod) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 |
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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. THE SHEETS PRESENTED AS "BA" 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. THE SHEETS PRESENTED AS "CA" 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. THE SHEETS PRESENTED AS "DA" 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 |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zuo.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zuo.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zuo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3zuo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3zuo_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 3zuo_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/3zuo ftp://data.pdbj.org/pub/pdb/validation_reports/zu/3zuo | HTTPS FTP |
-Related structure data
Related structure data | 3zuiSC 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 16804.586 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ORNITHODOROS MOUBATA (arthropod) / Organ: SALIVARY GLAND / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): WCM105 / References: UniProt: Q5YD59 #2: Chemical | ChemComp-LTB / #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: 2.14 Å3/Da / Density % sol: 42.62 % / Description: NONE |
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Crystal grow | pH: 8.4 Details: 21% PEG 4000, 0.2 M SODIUM ACETATE, TRIS 0.1 M PH 8.4. |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.00384 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00384 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→112.79 Å / Num. obs: 46060 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 27.45 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.86→1.96 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 82.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZUI Resolution: 1.86→61.06 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.9075 / SU R Cruickshank DPI: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.178 / SU Rfree Blow DPI: 0.144 / SU Rfree Cruickshank DPI: 0.147 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 35.22 Å2
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Refine analyze | Luzzati coordinate error obs: 0.275 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→61.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.91 Å / Total num. of bins used: 20
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