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- PDB-3zui: OMCI in complex with palmitoleic acid -

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Basic information

Entry
Database: PDB / ID: 3zui
TitleOMCI in complex with palmitoleic acid
ComponentsCOMPLEMENT INHIBITOR
KeywordsIMMUNE SYSTEM / SOFT TICK / ARGASID TICK / C5 / LIPOCALIN COMPLEMENT
Function / homologyCalycin beta-barrel core domain / Calycin / Lipocalin / toxin activity / Beta Barrel / extracellular region / Mainly Beta / PALMITOLEIC ACID / Complement inhibitor
Function and homology information
Biological speciesORNITHODOROS MOUBATA (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsRoversi, 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
DepositionJul 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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)17,0592
Polymers16,8051
Non-polymers2541
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.430, 51.890, 68.400
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: 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 / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsPALIMITOLEIC ACID (PAM): IDENTIFIED BY MASS SPECTROMETRY AS 60% OF THE FATTY ACID IN THE BINDING POCKET

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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: 2.35 Å3/Da / Density % sol: 47.7 % / Description: NONE
Crystal growpH: 8.5 / Details: 30% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS PH 8.5.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.71→1.81 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 62.2

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CM4

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 783 4.99 %RANDOM
Rwork0.1969 ---
obs0.1981 15678 88.71 %-
Displacement parametersBiso mean: 25.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.6855 Å20 Å20 Å2
2---5.846 Å20 Å2
3---5.1605 Å2
Refine analyzeLuzzati coordinate error obs: 0.195 Å
Refinement stepCycle: LAST / Resolution: 1.71→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 0 18 146 1307
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0062264HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.934062HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d493SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes41HARMONIC2
X-RAY DIFFRACTIONt_gen_planes328HARMONIC5
X-RAY DIFFRACTIONt_it2263HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion15.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion147SEMIHARMONIC5
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_contact2359SEMIHARMONIC4
LS refinement shellResolution: 1.71→1.83 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2381 99 5.27 %
Rwork0.2235 1781 -
all0.2242 1880 -
obs--88.71 %

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