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- PDB-5ni6: Crystal structure of human LTA4H mutant D375N in complex with LTA4 -

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Basic information

Entry
Database: PDB / ID: 5ni6
TitleCrystal structure of human LTA4H mutant D375N in complex with LTA4
ComponentsLeukotriene A-4 hydrolase
KeywordsHYDROLASE / Metallopeptidase / epoxide hydrolase / leukotriene A4
Function / homology
Function and homology information


leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / 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 / protein metabolic process ...leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / 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 / protein metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / 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 / extracellular exosome / zinc ion binding / 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 ...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, 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 / 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
ACETIC ACID / Chem-DJ3 / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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)71,0427
Polymers70,1921
Non-polymers8506
Water14,862825
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-8 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.130, 87.450, 99.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 831 molecules

#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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / 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: 277 K / Method: liquid diffusion / pH: 7
Details: 22% (w/v) PEG 8000, 100 mM imidazole pH 7.0, 100 mM sodium acetate, 5 mM YbCl3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.54→43.229 Å / Num. obs: 100716 / % possible obs: 99.47 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1045 / Rpim(I) all: 0.04466 / Net I/σ(I): 10.35
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.729 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 9575 / CC1/2: 0.432 / Rpim(I) all: 0.7528 / % possible all: 95.77

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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: 1.54→43.229 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1908 5063 5.03 %
Rwork0.1581 --
obs0.1597 100690 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→43.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 34 825 5719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085225
X-RAY DIFFRACTIONf_angle_d0.9477100
X-RAY DIFFRACTIONf_dihedral_angle_d15.8711963
X-RAY DIFFRACTIONf_chiral_restr0.054786
X-RAY DIFFRACTIONf_plane_restr0.007917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.55750.31891530.3192773X-RAY DIFFRACTION88
1.5575-1.57580.3511860.29893121X-RAY DIFFRACTION100
1.5758-1.59510.31291680.29723165X-RAY DIFFRACTION100
1.5951-1.61530.28741790.29123145X-RAY DIFFRACTION100
1.6153-1.63650.28531690.28643186X-RAY DIFFRACTION100
1.6365-1.65890.29121830.27083145X-RAY DIFFRACTION100
1.6589-1.68260.33151640.26033155X-RAY DIFFRACTION100
1.6826-1.70770.28872040.24533161X-RAY DIFFRACTION100
1.7077-1.73440.26271750.23273157X-RAY DIFFRACTION100
1.7344-1.76290.27161590.21723170X-RAY DIFFRACTION100
1.7629-1.79330.23431830.20633165X-RAY DIFFRACTION100
1.7933-1.82590.22921630.19573176X-RAY DIFFRACTION100
1.8259-1.8610.20971560.17663230X-RAY DIFFRACTION100
1.861-1.8990.20941730.1683153X-RAY DIFFRACTION100
1.899-1.94030.17021690.16753156X-RAY DIFFRACTION100
1.9403-1.98540.20741630.17473199X-RAY DIFFRACTION100
1.9854-2.03510.19361570.17093211X-RAY DIFFRACTION100
2.0351-2.09010.21041550.15763209X-RAY DIFFRACTION100
2.0901-2.15160.18731660.14973159X-RAY DIFFRACTION100
2.1516-2.2210.17341400.14223241X-RAY DIFFRACTION100
2.221-2.30040.1671710.13763225X-RAY DIFFRACTION100
2.3004-2.39250.1731850.13233155X-RAY DIFFRACTION100
2.3925-2.50140.18631590.12943235X-RAY DIFFRACTION100
2.5014-2.63320.15951530.1323237X-RAY DIFFRACTION100
2.6332-2.79820.17011810.1313211X-RAY DIFFRACTION100
2.7982-3.01420.17421850.13463239X-RAY DIFFRACTION100
3.0142-3.31740.16551680.13813220X-RAY DIFFRACTION100
3.3174-3.79720.1651620.13713278X-RAY DIFFRACTION100
3.7972-4.78310.13641600.12493297X-RAY DIFFRACTION100
4.7831-43.24610.21681740.17563453X-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)
11.0385-0.6234-0.08851.84610.44610.7161-0.0765-0.1447-0.05750.38830.0764-0.04750.13910.0129-0.00110.2275-0.0029-0.01270.14950.01320.1218-35.6391-14.68379.5892
20.66620.024-0.17320.97760.0390.7846-0.0730.09230.0427-0.08490.0161-0.1107-0.00320.07950.05760.1723-0.0276-0.01020.20220.0070.1818-35.42984.8686-10.0577
30.46880.6711-0.15023.8281-1.18071.30860.0448-0.02870.03480.222-0.0336-0.0465-0.0270.0274-0.00550.1167-0.0047-0.0160.159-0.02950.1525-29.86925.53135.4021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 3:208
2X-RAY DIFFRACTION2chain A and resi 209:465
3X-RAY DIFFRACTION3chain A and resi 466:610

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