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- PDB-2xpz: Structure of native yeast LTA4 hydrolase -

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Basic information

Entry
Database: PDB / ID: 2xpz
TitleStructure of native yeast LTA4 hydrolase
ComponentsLEUKOTRIENE A-4 HYDROLASE
KeywordsHYDROLASE
Function / homology
Function and homology information


Synthesis of Leukotrienes (LT) and Eoxins (EX) / Biosynthesis of protectins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / cellular lipid metabolic process / leukotriene-A4 hydrolase activity / soluble epoxide hydrolase / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases ...Synthesis of Leukotrienes (LT) and Eoxins (EX) / Biosynthesis of protectins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / cellular lipid metabolic process / leukotriene-A4 hydrolase activity / soluble epoxide hydrolase / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / epoxide hydrolase activity / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / Neutrophil degranulation / protein catabolic process / proteolysis / zinc ion binding / nucleus / cytoplasm / 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
(R,R)-2,3-BUTANEDIOL / Leucine aminopeptidase 2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHelgstrand, C. / Hasan, M. / Usyal, H. / Haeggstrom, J.Z. / Thunnissen, M.M.G.M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: A Leukotriene A(4) Hydrolase-Related Aminopeptidase from Yeast Undergoes Induced Fit Upon Inhibitor Binding.
Authors: Helgstrand, C. / Hasan, M. / Usyal, H. / Haeggstrom, J.Z. / Thunnissen, M.M.G.M.
History
DepositionAug 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Apr 24, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.5May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)74,5814
Polymers72,8961
Non-polymers1,6853
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.833, 98.096, 99.197
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


Mass: 72896.055 Da / Num. of mol.: 1 / Fragment: RESIDUES 40-671
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q10740, leukotriene-A4 hydrolase
#2: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.39 Å3/Da / Density % sol: 48.54 % / Description: NONE
Crystal growMethod: liquid diffusion
Details: THE CRYSTALS ARE GROWN IN LIQUID-LIQUID DIFFUSION EXPERIMENTS USING MELTING POINT CAPILLARIES IN WHICH 5 UL PROTEIN (6 MG/ML) IN 10 MM TRIS PH 8.5 IS LAYERED ON 5 UL 14% PEG 8000 AND 100 MM TRIS PH 7.3.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -H,L,K / Fraction: 0.06
ReflectionResolution: 2.3→15 Å / Num. obs: 29531 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.2
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 1.4 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL NATIVE SCLTA4, P3221

Resolution: 2.3→14.981 Å / σ(F): 0.12 / Phase error: 29.14 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2691 1241 4.3 %
Rwork0.1902 --
obs0.193 29056 93.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.976 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4676 Å20 Å20 Å2
2---4.0416 Å20 Å2
3----0.4261 Å2
Refinement stepCycle: LAST / Resolution: 2.3→14.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5112 0 22 474 5608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085269
X-RAY DIFFRACTIONf_angle_d1.1177142
X-RAY DIFFRACTIONf_dihedral_angle_d18.7581910
X-RAY DIFFRACTIONf_chiral_restr0.068769
X-RAY DIFFRACTIONf_plane_restr0.004918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3034-2.40740.35791280.30783004X-RAY DIFFRACTION79
2.4074-2.53310.41281500.32073368X-RAY DIFFRACTION88
2.5331-2.68990.34681420.27713468X-RAY DIFFRACTION91
2.6899-2.89470.28311730.24793459X-RAY DIFFRACTION90
2.8947-3.18050.29971390.2143530X-RAY DIFFRACTION92
3.1805-3.62850.25861500.16313594X-RAY DIFFRACTION93
3.6285-4.52630.20951360.12633643X-RAY DIFFRACTION93
4.5263-11.6310.22351590.13683693X-RAY DIFFRACTION91
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)
10.27920.24110.2261.08210.69070.46290.1186-0.1020.02370.4898-0.0367-0.05260.1663-0.0173-0.07510.2801-0.0424-0.00910.0348-0.03250.018513.632537.056334.5782
20.23760.4070.26850.72280.3570.7120.0202-0.00920.02750.1944-0.0113-0.0713-0.10730.0498-0.00810.1398-0.0101-0.04450.0617-0.0630.122824.851645.61234.2463
30.11020.35710.0941.160.29440.80430.01640.0013-0.03590.02650.029-0.1379-0.1220.1182-0.05130.0173-0.04350.0243-0.0017-0.00740.041818.937737.357719.0203
40.1644-0.0546-0.13921.31691.5371.82890.03080.01440.0086-0.5438-0.0264-0.021-0.5341-0.0505-0.00430.92320.01430.0110.74940.00150.75429.596748.96645.1417
50.10160.1157-0.12710.8960.31840.73320.01370.0308-0.03350.3345-0.1241-0.00850.3573-0.03620.11510.173-0.10010.105-0.1030.0564-0.04475.861715.387722.4962
60.3423-0.4218-0.53090.54880.71750.9627-0.2127-0.1025-0.01780.31230.13860.04870.44180.19790.06770.24220.12470.04970.0727-0.0330.04924.13893.03888.6991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 40:98)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 102:147)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 148:223)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 224:230)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 231:559)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 560:671)

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