+Open data
-Basic information
Entry | Database: PDB / ID: 2cm4 | ||||||
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Title | The complement inhibitor OmCI in complex with ricinoleic acid | ||||||
Components | COMPLEMENT INHIBITOR | ||||||
Keywords | INHIBITOR / ORNITHODOROS MOUBATA / C5 / TICK / OMCI / LIPOCALIN / COMPLEMENT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ORNITHODOROS MOUBATA (arthropod) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Roversi, P. / Johnson, S. / Lissina, O. / Paesen, G.C. / Boland, W. / Nunn, M.A. / Lea, S.M. | ||||||
Citation | 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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 | 2cm4.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cm4.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/2cm4 ftp://data.pdbj.org/pub/pdb/validation_reports/cm/2cm4 | HTTPS FTP |
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-Related structure data
Related structure data | 2cm9C 1qftS C: citing same article (ref.) S: Starting model for refinement |
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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: 16832.639 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: DOUBLE MUTATION TO PREVENT THE YEAST EXPRESSION SYSTEM TO INTRODUCE GLYCOSYLATION Source: (gene. exp.) ORNITHODOROS MOUBATA (arthropod) / Production host: PICHIA METHANOLICA (fungus) / Strain (production host): PMAD11 / References: UniProt: Q5YD59 | ||
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#2: Chemical | ChemComp-ACT / | ||
#3: Chemical | ChemComp-RCL / | ||
#4: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | NO SIGNAL TAG 1-18 IN THIS CONSTRUCT MUTATIONS N78Q, N102Q | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.4 % Description: AMORE WAS RUN FROM THE CASPR SERVER AT WWW.IGS.CNRS- MRS.FR SLASH CASPR2 |
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Crystal grow | pH: 4.6 Details: 30% PEG 4000 0.1 M SODIUM ACETATE PH 4.6 0.2 M AMMONIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9757 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 31, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9757 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40.9 Å / Num. obs: 110764 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 1.58 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.6 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QFT Resolution: 1.9→40.9 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: TNT WAS RUN AGAINST MAXIMUM LIKELIHOOD WITHIN BUSTER-TNT VERSION 1.3.0
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 11 Å2 / ksol: 0.419 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40.9 Å
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Refine LS restraints |
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