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- PDB-5ni2: Crystal structure of human LTA4H mutant E271A in complex with LTA... -

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Basic information

Entry
Database: PDB / ID: 5ni2
TitleCrystal structure of human LTA4H mutant E271A in complex with LTA4 (crystal form I)
ComponentsLeukotriene A-4 hydrolase
KeywordsHYDROLASE / Metallopeptidase / epoxide hydrolase / leukotriene A4
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
Chem-DJ3 / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.501 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 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8655
Polymers70,1351
Non-polymers7304
Water11,512639
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-8 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.710, 84.610, 133.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-1139-

HOH

21A-1433-

HOH

31A-1437-

HOH

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Components

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


Mass: 70134.820 Da / Num. of mol.: 1 / Mutation: E271A
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: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Yb
#4: Chemical ChemComp-DJ3 / 5S-5,6-oxido-7,9-trans-11,14-cis-eicosatetraenoic acid


Mass: 318.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 277 K / Method: liquid diffusion / pH: 6.7
Details: 22% (w/v) PEG 8000, 100 mM imidazole pH 6.7, 5 mM YbCl3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→39.37 Å / Num. obs: 122621 / % possible obs: 99.47 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09879 / Rpim(I) all: 0.04128 / Net I/σ(I): 9.25
Reflection shellResolution: 1.5→1.56 Å / Redundancy: 6.7 % / Rmerge(I) obs: 2.077 / Mean I/σ(I) obs: 0.67 / Num. unique obs: 11695 / CC1/2: 0.285 / Rpim(I) all: 0.8572 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.501→39.369 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1963 6121 5.01 %
Rwork0.1722 --
obs0.1734 122196 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.501→39.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4848 0 26 639 5513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085116
X-RAY DIFFRACTIONf_angle_d0.9956951
X-RAY DIFFRACTIONf_dihedral_angle_d14.3321934
X-RAY DIFFRACTIONf_chiral_restr0.053773
X-RAY DIFFRACTIONf_plane_restr0.006887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5012-1.51830.371860.36723526X-RAY DIFFRACTION91
1.5183-1.53610.35052120.35683763X-RAY DIFFRACTION98
1.5361-1.55490.35282050.33943803X-RAY DIFFRACTION100
1.5549-1.57450.30882090.31583848X-RAY DIFFRACTION99
1.5745-1.59530.3241900.30653840X-RAY DIFFRACTION100
1.5953-1.61710.30562190.29923822X-RAY DIFFRACTION100
1.6171-1.64020.31021950.28083846X-RAY DIFFRACTION100
1.6402-1.66470.29342170.26933865X-RAY DIFFRACTION100
1.6647-1.69070.2892000.25713835X-RAY DIFFRACTION100
1.6907-1.71840.25062080.24843868X-RAY DIFFRACTION100
1.7184-1.74810.24882080.24823818X-RAY DIFFRACTION100
1.7481-1.77980.27741950.24533876X-RAY DIFFRACTION100
1.7798-1.81410.2571890.23163840X-RAY DIFFRACTION100
1.8141-1.85110.2412000.20323874X-RAY DIFFRACTION100
1.8511-1.89140.22262150.19323858X-RAY DIFFRACTION100
1.8914-1.93530.21232060.19683870X-RAY DIFFRACTION100
1.9353-1.98370.24432020.18313833X-RAY DIFFRACTION99
1.9837-2.03740.18832160.17223847X-RAY DIFFRACTION100
2.0374-2.09730.19522120.16533876X-RAY DIFFRACTION100
2.0973-2.1650.20422110.16453883X-RAY DIFFRACTION100
2.165-2.24240.17942070.15443868X-RAY DIFFRACTION100
2.2424-2.33220.15721730.15243920X-RAY DIFFRACTION100
2.3322-2.43830.16381930.15373902X-RAY DIFFRACTION100
2.4383-2.56680.19382270.15683899X-RAY DIFFRACTION100
2.5668-2.72760.19182160.15543917X-RAY DIFFRACTION100
2.7276-2.93810.19791860.15543921X-RAY DIFFRACTION100
2.9381-3.23370.19992130.16863921X-RAY DIFFRACTION100
3.2337-3.70130.17972120.15783927X-RAY DIFFRACTION100
3.7013-4.66210.15471870.13514031X-RAY DIFFRACTION100
4.6621-39.38230.18612120.17824178X-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)
10.32650.09990.00650.12530.07970.3030.1216-0.039-0.0836-0.16950.25940.23730.4156-0.33470.23810.4932-0.1878-0.19250.32660.17340.4224-1.911852.713221.9584
20.11590.0598-0.11950.4302-0.29480.69650.031-0.0971-0.0757-0.01790.0570.04490.19430.0160.00050.2490.0231-0.03130.26970.0490.284320.672965.724331.1478
30.18690.11-0.03090.399-0.1340.3692-0.00090.0335-0.0028-0.11080.06430.02310.04720.043-00.24920.0002-0.01060.29370.03010.239723.789182.058610.8433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 3:208
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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