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

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Open data


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Basic information

Entry
Database: PDB / ID: 5nid
TitleCrystal structure of human LTA4H mutant D375N in open conformation (crystal form II)
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 / 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
Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.568 Å
AuthorsStsiapanava, A.
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2572
Polymers70,1921
Non-polymers651
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-36 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.930, 153.930, 76.790
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.: 392 / 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: 2.56 Å3/Da / Density % sol: 52 %
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: 0.9762 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: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.568→44.44 Å / Num. obs: 95099 / % possible obs: 99.93 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05894 / Rpim(I) all: 0.02343 / Net I/σ(I): 13.67
Reflection shellResolution: 1.568→1.624 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.882 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 9558 / CC1/2: 0.374 / Rpim(I) all: 0.785 / % possible all: 99.74

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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: 1.568→44.436 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.15
RfactorNum. reflection% reflection
Rfree0.2098 4840 5.09 %
Rwork0.1821 --
obs0.1836 95071 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.64 Å2
Refinement stepCycle: LAST / Resolution: 1.568→44.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 1 392 5261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015094
X-RAY DIFFRACTIONf_angle_d0.9566936
X-RAY DIFFRACTIONf_dihedral_angle_d15.1791898
X-RAY DIFFRACTIONf_chiral_restr0.057774
X-RAY DIFFRACTIONf_plane_restr0.007888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.568-1.58580.50451600.44762987X-RAY DIFFRACTION100
1.5858-1.60450.40151630.41993036X-RAY DIFFRACTION100
1.6045-1.62410.43111610.40043032X-RAY DIFFRACTION100
1.6241-1.64460.43531560.37822935X-RAY DIFFRACTION100
1.6446-1.66630.41121620.35133005X-RAY DIFFRACTION100
1.6663-1.68910.36971600.33633029X-RAY DIFFRACTION100
1.6891-1.71320.3621650.3073040X-RAY DIFFRACTION100
1.7132-1.73880.33491640.29183015X-RAY DIFFRACTION100
1.7388-1.7660.31671600.27372977X-RAY DIFFRACTION100
1.766-1.79490.2871530.26273000X-RAY DIFFRACTION100
1.7949-1.82590.28991240.24773040X-RAY DIFFRACTION100
1.8259-1.85910.26551470.24153051X-RAY DIFFRACTION100
1.8591-1.89480.27141670.23092996X-RAY DIFFRACTION100
1.8948-1.93350.25181320.22173054X-RAY DIFFRACTION100
1.9335-1.97560.22041550.23133010X-RAY DIFFRACTION100
1.9756-2.02150.23061650.20973027X-RAY DIFFRACTION100
2.0215-2.07210.2311600.20972983X-RAY DIFFRACTION100
2.0721-2.12810.23231490.20243006X-RAY DIFFRACTION100
2.1281-2.19070.20871710.18993019X-RAY DIFFRACTION100
2.1907-2.26140.2092040.18812950X-RAY DIFFRACTION100
2.2614-2.34220.22911470.19043014X-RAY DIFFRACTION100
2.3422-2.4360.19591650.18763020X-RAY DIFFRACTION100
2.436-2.54690.2251490.17613007X-RAY DIFFRACTION100
2.5469-2.68110.21421620.17412997X-RAY DIFFRACTION100
2.6811-2.84910.17721480.18223051X-RAY DIFFRACTION100
2.8491-3.0690.21682010.18742958X-RAY DIFFRACTION100
3.069-3.37780.19691870.17692980X-RAY DIFFRACTION100
3.3778-3.86630.20251940.14852985X-RAY DIFFRACTION100
3.8663-4.87020.15971460.12833036X-RAY DIFFRACTION100
4.8702-44.45360.17791630.16172991X-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)
11.69720.0775-0.37152.36820.67931.10080.0424-0.2923-0.2070.5959-0.1011-0.31220.3072-0.04710.06270.3646-0.0399-0.07530.29720.08990.220521.4551246.3435-23.4226
20.9903-0.1294-0.21111.71640.61170.7912-0.01160.04650.0805-0.21790.0703-0.3041-0.13140.0301-0.05790.2895-0.0179-0.01740.28210.04520.352530.8212267.3698-38.8135
33.28551.0056-0.53831.5475-0.81812.5665-0.40140.53440.18-1.77640.3155-0.1088-0.005-0.29990.04691.1824-0.06440.0690.5260.08170.42627.6595257.0199-65.0812
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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