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- PDB-5nie: Crystal structure of human LTA4H mutant R563A in open conformation -

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Basic information

Entry
Database: PDB / ID: 5nie
TitleCrystal structure of human LTA4H mutant R563A in open conformation
ComponentsLeukotriene A-4 hydrolase
KeywordsHYDROLASE / Metallopeptidase / epoxide hydrolase / open conformation
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
Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-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 / Zincin-like - #30 / Zincin-like ...Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-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 / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / 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 / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 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: 2.603 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: 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
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
B: Leukotriene A-4 hydrolase
C: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,5166
Polymers210,3203
Non-polymers1963
Water2,774154
1
A: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1722
Polymers70,1071
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1722
Polymers70,1071
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1722
Polymers70,1071
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.970, 132.150, 320.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 70106.734 Da / Num. of mol.: 3 / Mutation: R563A
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.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% (w/v) PEG MME 5000, 100 mM MES monohydrate pH 6.0, 150 mM Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.603→49.473 Å / Num. obs: 64086 / % possible obs: 92.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 32.42 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.08061 / Net I/σ(I): 5.9
Reflection shellResolution: 2.603→2.696 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.109 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 5413 / CC1/2: 0.471 / Rpim(I) all: 0.5757 / % possible all: 80

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NI2

5ni2


Resolution: 2.603→49.473 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.38
RfactorNum. reflection% reflection
Rfree0.2909 3105 4.85 %
Rwork0.2351 --
obs0.2378 64057 92.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.83 Å2
Refinement stepCycle: LAST / Resolution: 2.603→49.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14522 0 3 155 14680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314921
X-RAY DIFFRACTIONf_angle_d0.61420273
X-RAY DIFFRACTIONf_dihedral_angle_d12.018944
X-RAY DIFFRACTIONf_chiral_restr0.0452264
X-RAY DIFFRACTIONf_plane_restr0.0042581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.603-2.64370.38661170.37582284X-RAY DIFFRACTION79
2.6437-2.6870.39521230.37132364X-RAY DIFFRACTION81
2.687-2.73340.43561260.35272482X-RAY DIFFRACTION83
2.7334-2.7830.37971260.34592352X-RAY DIFFRACTION82
2.783-2.83660.42751270.35432477X-RAY DIFFRACTION84
2.8366-2.89450.42441330.37312631X-RAY DIFFRACTION88
2.8945-2.95740.39481290.3312606X-RAY DIFFRACTION90
2.9574-3.02620.39061400.3162697X-RAY DIFFRACTION92
3.0262-3.10180.32681390.30332720X-RAY DIFFRACTION92
3.1018-3.18570.33551420.30232746X-RAY DIFFRACTION94
3.1857-3.27940.34561460.28982849X-RAY DIFFRACTION95
3.2794-3.38530.37321350.27592845X-RAY DIFFRACTION96
3.3853-3.50620.34521540.26542888X-RAY DIFFRACTION97
3.5062-3.64660.31481430.23572906X-RAY DIFFRACTION98
3.6466-3.81250.25991510.22042899X-RAY DIFFRACTION98
3.8125-4.01340.26731480.20992964X-RAY DIFFRACTION98
4.0134-4.26470.25281490.19122915X-RAY DIFFRACTION98
4.2647-4.59380.22841490.16882933X-RAY DIFFRACTION98
4.5938-5.05560.2041500.16023015X-RAY DIFFRACTION99
5.0556-5.78620.25241560.17813060X-RAY DIFFRACTION99
5.7862-7.28630.25021560.20323071X-RAY DIFFRACTION100
7.2863-49.48230.21111660.17483248X-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)
1-0.09750.2473-0.13780.4509-0.03170.3882-0.0456-0.0379-0.0175-0.06960.05750.03190.23660.02620.00150.2548-0.0261-0.01280.27470.0120.2525-24.8194-44.737884.9945
20.37410.0457-0.66650.0109-0.36570.68510.02840.00040.01280.0055-0.0457-0.0416-0.0148-0.0401-0.00010.24690.0165-0.03330.3073-0.0150.2897-5.0239-26.077480.5741
30.22850.2993-0.10210.3869-0.02430.4116-0.09780.05310.0148-0.01780.1183-0.08680.06950.042600.308-0.0356-0.00520.4280.05690.347-9.7663-19.462353.0702
40.3874-0.15670.28980.64680.24680.83590.0477-0.0515-0.00050.0506-0.0916-0.0879-0.06820.1549-00.3225-0.05090.01650.37280.00040.36548.7173-59.202844.4144
50.0628-0.30520.16780.3769-0.47690.35030.0970.05250.0008-0.07890.0196-0.0132-0.0089-0.0408-00.4546-0.00830.04850.3027-0.02160.3561-9.6551-64.455124.5432
60.2816-0.05280.2220.6195-0.16620.27780.2584-0.01320.145-0.3172-0.0907-0.06740.06570.01860.00210.643-0.01480.0460.3337-0.00630.3978-2.3963-44.57945.1455
70.15860.27820.30920.9059-0.1430.7867-0.06720.0511-0.0322-0.15820.0642-0.114-0.04580.1033-00.4798-0.00780.0630.3331-0.0020.3111-5.152520.473816.4534
8-0.15910.2709-0.46480.7698-0.0323-0.13430.0023-0.0231-0.042-0.1129-0.0210.04360.0183-0.0380.00010.32390.0452-0.02840.3677-0.02720.3151-24.62526.010729.5717
90.4718-0.4251-0.29060.73830.0757-0.0976-0.0118-0.0487-0.04750.0572-0.0759-0.13720.1482-0.021-0.00060.4325-0.03010.06970.2275-0.00890.3397-16.3573-21.295523.5982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 4:208
2X-RAY DIFFRACTION2chain A and resi 209:465 or (chain A and resi 900 and resname ZN)
3X-RAY DIFFRACTION3chain A and resi 466:609
4X-RAY DIFFRACTION4chain B and resi 3:208
5X-RAY DIFFRACTION5chain B and resi 209:465 or (chain B and resi 900 and resname ZN)
6X-RAY DIFFRACTION6chain B and resi 466:609
7X-RAY DIFFRACTION7chain C and resi 4:208
8X-RAY DIFFRACTION8chain C and resi 209:465 or (chain C and resi 900 and resname ZN)
9X-RAY DIFFRACTION9chain C and resi 466:609

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