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- PDB-5hae: Crystal structure of LTBP1 LTC4 complex collected on an in-house ... -

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Basic information

Entry
Database: PDB / ID: 5hae
TitleCrystal structure of LTBP1 LTC4 complex collected on an in-house source
ComponentsLipocalin AI-4
KeywordsTRANSPORT PROTEIN / lipocalin / salivary / Rhodnius
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 / FOURIER SYNTHESIS / Resolution: 2.002 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 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.source / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-6 kcal/mol
Surface area8140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.269, 58.388, 36.018
Angle α, β, γ (deg.)90.000, 103.750, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): 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


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


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris, pH 8, 30% PEG 6000 / PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9042 / % possible obs: 96.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.31 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.036 / Rrim(I) all: 0.074 / Χ2: 2.666 / Net I/av σ(I): 37.619 / Net I/σ(I): 20.6 / Num. measured all: 35561
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.80.1364220.980.0770.1572.11493.8
2.03-2.073.80.1384440.9770.080.162.0692.9
2.07-2.114.10.1194510.9840.0650.1362.02495.1
2.11-2.1540.1184370.9820.0660.1362.24895.2
2.15-2.24.10.114330.9840.060.1262.12194.7
2.2-2.253.90.0974450.9870.0550.1122.28995.1
2.25-2.3140.0984480.9870.0550.1132.28195.5
2.31-2.373.80.0874460.990.050.12.24897.2
2.37-2.443.90.0934650.9870.0530.1072.46996.3
2.44-2.523.90.0884330.9910.0490.1022.42796.4
2.52-2.6140.0814600.9890.0460.0942.40997.3
2.61-2.713.90.0784470.9880.0450.0912.67195.7
2.71-2.8440.0724600.990.040.0822.84597.5
2.84-2.994.10.0664530.9940.0370.0763.02196.8
2.99-3.1740.0624410.9950.0340.0713.13496.7
3.17-3.4240.0584720.9930.0320.0663.29698.1
3.42-3.763.90.0534640.9950.030.0623.39698.1
3.76-4.313.90.0514700.9960.0290.0593.56798.5
4.31-5.433.90.0454660.9970.0250.0523.23998.3
5.43-503.90.0454850.9950.0260.0523.23998.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.002→34.986 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 479 5.31 %
Rwork0.1463 8547 -
obs0.1493 9026 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.63 Å2 / Biso mean: 20.6966 Å2 / Biso min: 7.78 Å2
Refinement stepCycle: final / Resolution: 2.002→34.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 43 168 1390
Biso mean--21.34 27.92 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061256
X-RAY DIFFRACTIONf_angle_d1.1041689
X-RAY DIFFRACTIONf_chiral_restr0.042183
X-RAY DIFFRACTIONf_plane_restr0.004220
X-RAY DIFFRACTIONf_dihedral_angle_d16.538456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0016-2.29120.23951540.14552775292994
2.2912-2.88640.22061610.16252839300097
2.8864-34.99140.17991640.13832933309798
Refinement TLS params.Method: refined / Origin x: -6.1287 Å / Origin y: 5.8651 Å / Origin z: -9.9589 Å
111213212223313233
T0.0867 Å20.0019 Å2-0.005 Å2-0.0989 Å2-0.0125 Å2--0.0964 Å2
L1.3659 °2-0.104 °2-0.3517 °2-1.4074 °2-0.1903 °2--2.7765 °2
S-0.0579 Å °-0.0378 Å °0.0115 Å °0.0533 Å °0.0243 Å °-0.0358 Å °0.0622 Å °0.0006 Å °0.0265 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 156
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 221

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