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- PDB-5nia: Crystal structure of human LTA4H mutant D375N in open conformatio... -

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Basic information

Entry
Database: PDB / ID: 5nia
TitleCrystal structure of human LTA4H mutant D375N in open conformation (crystal form I)
ComponentsLeukotriene A-4 hydrolase
KeywordsHYDROLASE / Metallopeptidase / epoxide hydrolase / open conformation
Function / homology
Function and homology information


leukotriene-A4 hydrolase / tripeptide aminopeptidase / tripeptide aminopeptidase activity / leukotriene-A4 hydrolase activity / Biosynthesis of protectins / 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) ...leukotriene-A4 hydrolase / tripeptide aminopeptidase / tripeptide aminopeptidase activity / leukotriene-A4 hydrolase activity / Biosynthesis of protectins / 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) / protein metabolic process / epoxide hydrolase activity / leukotriene biosynthetic process / type I pneumocyte differentiation / peptide catabolic process / response to zinc ion / metalloaminopeptidase activity / aminopeptidase activity / lipid metabolic process / response to peptide hormone / tertiary granule lumen / peptidase activity / ficolin-1-rich granule lumen / Neutrophil degranulation / proteolysis / RNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal domain / Leukotriene A4 hydrolase/leucine aminopeptidase / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain ...Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal domain / Leukotriene A4 hydrolase/leucine aminopeptidase / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.764 Å
AuthorsStsiapanava, A.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Sweden
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Capturing LTA4 hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB4 synthesis.
Authors: Stsiapanava, A. / Samuelsson, B. / Haeggstrom, J.Z.
History
DepositionMar 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2572
Polymers70,1921
Non-polymers651
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-35 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.000, 153.000, 74.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 70191.867 Da / Num. of mol.: 1 / Mutation: D375N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTA4H, LTA4 / Plasmid: pT3MB4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P09960, leukotriene-A4 hydrolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 8% (w/v) PEG 20 000, 15% (w/v) PEG MME 550, 100 mM Hepes/MOPS pH 7.7-8.0, 15 mM CaCl2, 15 mM MgCl2
PH range: 7.7-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.764→44.167 Å / Num. obs: 64241 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1043 / Rpim(I) all: 0.04268 / Net I/σ(I): 9.28
Reflection shellResolution: 1.764→1.827 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.785 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 6342 / CC1/2: 0.394 / Rpim(I) all: 0.7518 / % possible all: 98.28

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NI2

5ni2


Resolution: 1.764→44.167 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.03
RfactorNum. reflection% reflection
Rfree0.2074 3271 5.09 %
Rwork0.1801 --
obs0.1816 64239 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.94 Å2
Refinement stepCycle: LAST / Resolution: 1.764→44.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 1 351 5220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155089
X-RAY DIFFRACTIONf_angle_d1.2296925
X-RAY DIFFRACTIONf_dihedral_angle_d16.7141887
X-RAY DIFFRACTIONf_chiral_restr0.068773
X-RAY DIFFRACTIONf_plane_restr0.01884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7642-1.79050.39731100.35722618X-RAY DIFFRACTION96
1.7905-1.81850.34761130.32342648X-RAY DIFFRACTION100
1.8185-1.84830.35721360.30162670X-RAY DIFFRACTION100
1.8483-1.88020.2981380.27812688X-RAY DIFFRACTION100
1.8802-1.91440.25881280.24582689X-RAY DIFFRACTION100
1.9144-1.95120.28241430.23352629X-RAY DIFFRACTION100
1.9512-1.9910.23291470.22482664X-RAY DIFFRACTION100
1.991-2.03430.23511370.2162619X-RAY DIFFRACTION100
2.0343-2.08160.23761240.21972697X-RAY DIFFRACTION100
2.0816-2.13370.24641510.20272644X-RAY DIFFRACTION100
2.1337-2.19140.25961530.18972631X-RAY DIFFRACTION100
2.1914-2.25590.21571690.18482624X-RAY DIFFRACTION100
2.2559-2.32870.22091340.18532646X-RAY DIFFRACTION100
2.3287-2.41190.22741500.18612676X-RAY DIFFRACTION100
2.4119-2.50850.20381250.17572660X-RAY DIFFRACTION100
2.5085-2.62260.22111530.17832653X-RAY DIFFRACTION100
2.6226-2.76090.22721280.18132648X-RAY DIFFRACTION100
2.7609-2.93380.20621460.18562661X-RAY DIFFRACTION100
2.9338-3.16030.22021850.1842628X-RAY DIFFRACTION100
3.1603-3.47820.20651410.17552634X-RAY DIFFRACTION100
3.4782-3.98120.18011900.15672603X-RAY DIFFRACTION100
3.9812-5.01480.14571210.13522685X-RAY DIFFRACTION100
5.0148-44.18110.18931490.16652653X-RAY DIFFRACTION100
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)
10.90230.608-0.48881.473-0.0030.1907-0.14450.2282-0.2317-0.14320.1258-0.02960.0564-0.1830.01850.258-0.0261-0.00770.286-0.060.222-28.04658.263-25.712
21.09140.5194-0.4090.5656-0.30860.32910.1833-0.044-0.00590.1284-0.1474-0.1013-0.12680.02280.00030.2539-0.0337-0.0260.22950.0070.2836-14.860826.6673-10.2289
30.5891-0.18660.17450.1421-0.20350.66710.5362-0.3746-0.64860.6078-0.2214-0.16260.19710.18140.25280.7085-0.1873-0.19980.48540.040.4721-22.225618.737715.3466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 1:208
2X-RAY DIFFRACTION2chain A and resi 209:465 or (resi 900 and resname ZN)
3X-RAY DIFFRACTION3chain A and resi 466:609

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