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- PDB-2cm4: The complement inhibitor OmCI in complex with ricinoleic acid -

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Basic information

Entry
Database: PDB / ID: 2cm4
TitleThe complement inhibitor OmCI in complex with ricinoleic acid
ComponentsCOMPLEMENT INHIBITOR
KeywordsINHIBITOR / ORNITHODOROS MOUBATA / C5 / TICK / OMCI / LIPOCALIN / COMPLEMENT
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / RICINOLEIC ACID / Complement inhibitor
Similarity search - Component
Biological speciesORNITHODOROS MOUBATA (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRoversi, P. / Johnson, S. / Lissina, O. / Paesen, G.C. / Boland, W. / Nunn, M.A. / Lea, S.M.
CitationJournal: 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
DepositionMay 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMPLEMENT INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1903
Polymers16,8331
Non-polymers3582
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.170, 55.520, 60.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein COMPLEMENT INHIBITOR / OMCI


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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-RCL / RICINOLEIC ACID


Mass: 298.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 78 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 102 TO GLN
Has protein modificationY
Sequence detailsNO SIGNAL TAG 1-18 IN THIS CONSTRUCT MUTATIONS N78Q, N102Q

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity 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
Crystal growpH: 4.6
Details: 30% PEG 4000 0.1 M SODIUM ACETATE PH 4.6 0.2 M AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9757
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9757 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.9→2 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
TNT5.6.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QFT

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
RfactorNum. reflection
Rwork0.169 -
all0.171 -
obs0.169 12440
Solvent computationSolvent model: BABINET SCALING / Bsol: 11 Å2 / ksol: 0.419 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 25 159 1321
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01411941
X-RAY DIFFRACTIONt_angle_deg0.82116013
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle16.3461
X-RAY DIFFRACTIONt_trig_c_planes0.009402
X-RAY DIFFRACTIONt_gen_planes0.0191665
X-RAY DIFFRACTIONt_it1.396119520
X-RAY DIFFRACTIONt_nbd0.024135
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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