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- PDB-3zuo: OMCI in complex with leukotriene B4 -

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Basic information

Entry
Database: PDB / ID: 3zuo
TitleOMCI in complex with leukotriene B4
ComponentsCOMPLEMENT INHIBITOR
KeywordsIMMUNE SYSTEM
Function / homologyCalycin beta-barrel core domain / Calycin / Lipocalin / toxin activity / Beta Barrel / extracellular region / Mainly Beta / LEUKOTRIENE B4 / Complement inhibitor
Function and homology information
Biological speciesORNITHODOROS MOUBATA (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COMPLEMENT INHIBITOR
B: COMPLEMENT INHIBITOR
C: COMPLEMENT INHIBITOR
D: COMPLEMENT INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5648
Polymers67,2184
Non-polymers1,3464
Water5,927329
1
A: COMPLEMENT INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1412
Polymers16,8051
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COMPLEMENT INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1412
Polymers16,8051
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: COMPLEMENT INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1412
Polymers16,8051
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: COMPLEMENT INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1412
Polymers16,8051
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.756, 112.789, 62.394
Angle α, β, γ (deg.)90.00, 101.89, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.81817, 0.0229, -0.57451), (0.0783, -0.98545, -0.1508), (-0.56962, -0.16837, 0.80448)16.0571, 30.3675, 8.0967
2given(0.79599, 0.22906, 0.56028), (0.20572, -0.9729, 0.10548), (0.56926, 0.03129, -0.82155)-25.136, 18.2481, 72.7584
3given(-0.9595, -0.27991, -0.0317), (-0.28166, 0.95519, 0.09097), (0.00481, 0.09621, -0.99534)-1.5937, -6.8209, 76.8239

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Components

#1: Protein
COMPLEMENT INHIBITOR / OMCI


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 / LEUKOTRIENE B4


Mass: 336.466 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H32O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.62 % / Description: NONE
Crystal growpH: 8.4
Details: 21% PEG 4000, 0.2 M SODIUM ACETATE, TRIS 0.1 M PH 8.4.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.00384
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00384 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.86→1.96 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 82.6

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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 3ZUI

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 2315 5.04 %RANDOM
Rwork0.2199 ---
obs0.2209 45917 96.87 %-
Displacement parametersBiso mean: 35.22 Å2
Baniso -1Baniso -2Baniso -3
1--9.0735 Å20 Å24.2977 Å2
2--6.693 Å20 Å2
3---2.3804 Å2
Refine analyzeLuzzati coordinate error obs: 0.275 Å
Refinement stepCycle: LAST / Resolution: 1.86→61.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 96 329 4955
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0069037HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8716214HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1956SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes158HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1339HARMONIC5
X-RAY DIFFRACTIONt_it9033HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion16.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion587SEMIHARMONIC5
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_contact9231SEMIHARMONIC4
LS refinement shellResolution: 1.86→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2824 135 4.88 %
Rwork0.2538 2633 -
all0.2552 2768 -
obs--96.87 %

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