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- PDB-5h9l: Crystal Structure of LTBP1 in complex with cleaved Leukotriene C4 -

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Basic information

Entry
Database: PDB / ID: 5h9l
TitleCrystal Structure of LTBP1 in complex with cleaved Leukotriene C4
ComponentsLipocalin AI-4
KeywordsTRANSPORT PROTEIN / lipocalin / leukotriene / Rhodnius / salivary
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / extracellular region
Similarity search - Function
Triabin/Procalin / Triabin / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-EAH / GLUTATHIONE / Lipocalin AI-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.37 Å
AuthorsAndersen, J.F.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structure and Ligand-Binding Mechanism of a Cysteinyl Leukotriene-Binding Protein from a Blood-Feeding Disease Vector.
Authors: Jablonka, W. / Pham, V. / Nardone, G. / Gittis, A. / Silva-Cardoso, L. / Atella, G.C. / Ribeiro, J.M. / Andersen, J.F.
History
DepositionDec 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipocalin AI-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5323
Polymers16,9051
Non-polymers6282
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.274, 58.388, 36.294
Angle α, β, γ (deg.)90.000, 103.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipocalin AI-4


Mass: 16904.709 Da / Num. of mol.: 1 / Fragment: UNP residues 18-173
Source method: isolated from a genetically manipulated source
Details: The first two residues of the polypeptide are disordered in the crystal
Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q7YT09
#2: Chemical ChemComp-EAH / (5S,7E,9E,11Z,14Z)-5-hydroxyicosa-7,9,11,14-tetraenoic acid


Mass: 320.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32O3
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, pH 8, 30 % PEG 6000 / PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 29238 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 10.41 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.049 / Rrim(I) all: 0.105 / Χ2: 1.339 / Net I/av σ(I): 18.509 / Net I/σ(I): 9.2 / Num. measured all: 135841
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.37-1.393.90.51514630.7470.2920.5950.7399.9
1.39-1.424.20.48414520.7660.270.5580.77199.9
1.42-1.454.40.43114360.8320.2330.4930.819100
1.45-1.484.60.39214650.8650.210.4470.86399.9
1.48-1.514.70.34114790.8960.1780.3860.992100
1.51-1.544.80.29214500.9180.150.331.076100
1.54-1.584.80.26514700.9320.1350.2981.22399.9
1.58-1.624.80.23514420.9480.120.2641.28499.9
1.62-1.674.80.21214460.9540.1080.2391.3899.9
1.67-1.734.80.18814810.9610.0970.2131.561100
1.73-1.794.80.16514520.9640.0850.1871.54899.9
1.79-1.864.80.14114460.9750.0730.1591.72100
1.86-1.944.80.12114660.9810.0620.1361.7399.8
1.94-2.054.80.10314520.9860.0530.1161.8199.7
2.05-2.174.80.09614680.9880.0490.1081.86199.7
2.17-2.344.70.08814540.990.0450.0991.8699.8
2.34-2.584.70.08114770.9910.0420.0911.49799.7
2.58-2.954.70.07114550.9930.0370.081.41899.6
2.95-3.724.70.05914850.9950.0310.0671.21299.9
3.72-504.40.05714990.9950.030.0651.08798.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 1.37→33.3 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 1478 5.06 %
Rwork0.1636 27738 -
obs0.1651 29216 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.7 Å2 / Biso mean: 18.5485 Å2 / Biso min: 4.62 Å2
Refinement stepCycle: final / Resolution: 1.37→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1170 0 43 194 1407
Biso mean--23.12 28.95 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061256
X-RAY DIFFRACTIONf_angle_d1.0821691
X-RAY DIFFRACTIONf_chiral_restr0.041184
X-RAY DIFFRACTIONf_plane_restr0.004220
X-RAY DIFFRACTIONf_dihedral_angle_d15.926458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.369-1.41310.2271280.2272484X-RAY DIFFRACTION99
1.4131-1.46370.25351330.20152514X-RAY DIFFRACTION100
1.4637-1.52230.22391390.18762510X-RAY DIFFRACTION100
1.5223-1.59150.21841320.16752500X-RAY DIFFRACTION100
1.5915-1.67540.17391300.1692529X-RAY DIFFRACTION100
1.6754-1.78040.19981340.16732535X-RAY DIFFRACTION100
1.7804-1.91790.18711330.16822541X-RAY DIFFRACTION100
1.9179-2.11080.17961370.15962508X-RAY DIFFRACTION100
2.1108-2.41620.1931420.16032536X-RAY DIFFRACTION100
2.4162-3.04380.20561270.17552525X-RAY DIFFRACTION100
3.0438-33.30.17071430.13862556X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6825-2.4925-0.56388.1477-0.44484.45540.0913-0.1020.08440.19-0.1176-0.1953-0.24560.13780.02520.10610.0032-0.00460.1425-0.0210.0564-5.139610.28533.139
24.4338-1.2865-0.70396.71142.34616.608-0.07-0.2909-0.06670.192-0.02750.45480.0865-0.59410.11910.0748-0.02330.01270.18540.01890.0904-17.85565.1689-8.3609
31.76460.585-1.75843.09310.83443.0870.00340.0301-0.07550.08520.055-0.18090.10890.2255-0.0650.06420.0074-0.01520.06690.01340.0681-1.00827.7876-17.7425
47.20111.3161-2.78814.589-0.70536.3187-0.1216-0.1703-0.06910.0293-0.0038-0.22830.30280.14040.11150.11430.01110.01190.0233-0.01180.0772-5.5827-4.0676-14.6361
56.2855-0.945-3.41314.99912.00966.2296-0.1820.1377-0.15790.1039-0.15620.09340.4392-0.30450.32980.0863-0.0047-0.02170.04460.02540.0294-7.8585-1.3261-3.5847
60.88520.4658-0.22330.83510.34612.4377-0.07450.0336-0.05910.05710.0218-0.06530.16970.03520.06010.05920.0010.00460.0452-0.00670.0594-6.40612.9449-8.1202
73.6712-0.8742.072.2847-1.32423.1974-0.0459-0.15050.04750.2710.0249-0.2692-0.10080.37950.04560.07360.0087-0.02470.1142-0.0040.08130.51867.9158-5.9664
81.3437-1.5153-1.56396.62213.75954.18120.02510.17620.1257-0.73130.1859-0.1055-0.387-0.1577-0.16310.09590.0182-0.02860.11880.00320.0496-10.660611.0765-22.9385
95.9112-4.0492-2.67993.87852.24793.1489-0.0738-0.20940.35690.16870.1802-0.1264-0.26740.0609-0.13880.1613-0.00540.00140.06570.01180.1181-7.12919.3898-13.6033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 15 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 29 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 46 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 62 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 63 through 78 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 112 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 113 through 127 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 128 through 135 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 136 through 155 )A0

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