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- PDB-7llq: Substrate-dependent divergence of leukotriene A4 hydrolase aminop... -

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Basic information

Entry
Database: PDB / ID: 7llq
TitleSubstrate-dependent divergence of leukotriene A4 hydrolase aminopeptidase activity
ComponentsLeukotriene A-4 hydrolase
KeywordsHYDROLASE / Leukotriene A4 hydrolase / 4MDM / Aminipeptidase / Activator
Function / homology
Function and homology information


leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / Biosynthesis of protectins / protein metabolic process / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins ...leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / Biosynthesis of protectins / protein metabolic process / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Synthesis of Leukotrienes (LT) and Eoxins (EX) / epoxide hydrolase activity / leukotriene biosynthetic process / response to zinc ion / peptide catabolic process / type I pneumocyte differentiation / metalloaminopeptidase activity / aminopeptidase activity / response to peptide hormone / lipid metabolic process / tertiary granule lumen / peptidase activity / ficolin-1-rich granule lumen / Neutrophil degranulation / proteolysis / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Leukotriene A4 hydrolase/leucine aminopeptidase / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / : / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain ...Leukotriene A4 hydrolase/leucine aminopeptidase / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / : / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Armadillo-type fold
Similarity search - Domain/homology
Chem-28T / 1-benzyl-4-methoxybenzene / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsLee, K.H. / Lee, S.H. / Shim, Y.M. / Paige, M. / Noble, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL132287 United States
CitationJournal: Sci Rep / Year: 2022
Title: Substrate-dependent modulation of the leukotriene A 4 hydrolase aminopeptidase activity and effect in a murine model of acute lung inflammation.
Authors: Lee, K.H. / Ali, N.F. / Lee, S.H. / Zhang, Z. / Burdick, M. / Beaulac, Z.J. / Petruncio, G. / Li, L. / Xiang, J. / Chung, E.M. / Foreman, K.W. / Noble, S.M. / Shim, Y.M. / Paige, M.
History
DepositionFeb 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukotriene A-4 hydrolase
B: Leukotriene A-4 hydrolase
C: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,68812
Polymers208,0923
Non-polymers1,5969
Water6,575365
1
A: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8964
Polymers69,3641
Non-polymers5323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8964
Polymers69,3641
Non-polymers5323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8964
Polymers69,3641
Non-polymers5323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.054, 138.054, 84.257
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein Leukotriene A-4 hydrolase / LTA-4 hydrolase / Leukotriene A(4) hydrolase / Tripeptide aminopeptidase LTA4H


Mass: 69363.969 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTA4H, LTA4 / Production host: Escherichia coli (E. coli)
References: UniProt: P09960, leukotriene-A4 hydrolase, tripeptide aminopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-N0Y / 1-benzyl-4-methoxybenzene


Mass: 198.260 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H14O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-28T / 1-{4-oxo-4-[(2S)-pyrrolidin-2-yl]butanoyl}-L-proline


Mass: 268.309 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H20N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 60-90 mM magnesium formate dihydrate, 20-25 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Dec 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.85→45.19 Å / Num. obs: 81035 / % possible obs: 96.8 % / Redundancy: 8.93 % / Biso Wilson estimate: 24.74 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.86
Reflection shellResolution: 2.85→2.91 Å / Rmerge(I) obs: 0.2716 / Num. unique obs: 40598

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
PROTEUMdata reduction
PROTEUMdata scaling
PROTEUMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MS6

4ms6


Resolution: 2.85→45.19 Å / SU ML: 0.3209 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.5914 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.229 3948 4.88 %
Rwork0.1995 76915 -
obs0.201 80863 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.6 Å2
Refinement stepCycle: LAST / Resolution: 2.85→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14580 0 105 365 15050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006415270
X-RAY DIFFRACTIONf_angle_d0.752220803
X-RAY DIFFRACTIONf_chiral_restr0.20272318
X-RAY DIFFRACTIONf_plane_restr0.0042653
X-RAY DIFFRACTIONf_dihedral_angle_d11.75835683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.880.29011440.26562759X-RAY DIFFRACTION95.56
2.88-2.920.2421510.2522710X-RAY DIFFRACTION95.69
2.92-2.960.27781200.24162651X-RAY DIFFRACTION96.48
2.96-30.27821600.23722895X-RAY DIFFRACTION96.13
3-3.040.27941400.23942632X-RAY DIFFRACTION95.92
3.04-3.090.26861360.222734X-RAY DIFFRACTION96.63
3.09-3.140.31771250.22522778X-RAY DIFFRACTION96.19
3.14-3.190.27521440.2132676X-RAY DIFFRACTION96.05
3.19-3.240.27171600.22842826X-RAY DIFFRACTION96.26
3.24-3.30.26131440.21792743X-RAY DIFFRACTION96.81
3.3-3.370.23491380.22042756X-RAY DIFFRACTION95.76
3.37-3.430.23221400.2212731X-RAY DIFFRACTION96.93
3.43-3.510.2411360.21252769X-RAY DIFFRACTION95.87
3.51-3.590.28271200.22272664X-RAY DIFFRACTION96.8
3.59-3.680.29341430.23682771X-RAY DIFFRACTION95.1
3.68-3.780.28011330.21692651X-RAY DIFFRACTION95.15
3.78-3.890.2221470.20082775X-RAY DIFFRACTION96.88
3.89-4.020.19591560.18742737X-RAY DIFFRACTION95.67
4.02-4.160.20751360.17882762X-RAY DIFFRACTION97.25
4.16-4.330.17351550.17272735X-RAY DIFFRACTION97.24
4.33-4.520.24571350.16532800X-RAY DIFFRACTION96.86
4.52-4.760.18781370.16242801X-RAY DIFFRACTION96.84
4.76-5.060.17181240.15932762X-RAY DIFFRACTION97.17
5.06-5.450.17151440.16362734X-RAY DIFFRACTION97.56
5.45-60.20961440.18492798X-RAY DIFFRACTION96.65
6-6.860.23741440.18342760X-RAY DIFFRACTION98.44
6.86-8.640.17521540.1732749X-RAY DIFFRACTION97.03
8.64-45.190.15391380.16112756X-RAY DIFFRACTION96.08

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