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- PDB-2xq0: Structure of yeast LTA4 hydrolase in complex with Bestatin -

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Basic information

Entry
Database: PDB / ID: 2xq0
TitleStructure of yeast LTA4 hydrolase in complex with Bestatin
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
Chem-BES / Leucine aminopeptidase 2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.955 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 1.4Dec 20, 2023Group: 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 / pdbx_struct_conn_angle / 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 / _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.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.value / _struct_conn.pdbx_dist_value / _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)73,4847
Polymers72,9681
Non-polymers5166
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.641, 99.874, 112.651
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: 72968.180 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)
Plasmid: PETM-11, PETM-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q10740, leukotriene-A4 hydrolase
#2: Chemical ChemComp-BES / 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID / BESTATIN


Mass: 308.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N2O4 / Comment: protease inhibitor*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.29 Å3/Da / Density % sol: 46.32 % / Description: NONE
Crystal growDetails: 15%GLYCEROL , 16.95% PEG 4000 , 8.5% ISOPROPANOL AND 0.1 M MMT BUFFER (PH 7.0) WITH 0.1 M BETAINE MONOHYDRATE AS AN ADDITIVE. THE RATIOS OF PROTEIN (9.6 MG/ML) WITH BESTATIN (6 MM), ...Details: 15%GLYCEROL , 16.95% PEG 4000 , 8.5% ISOPROPANOL AND 0.1 M MMT BUFFER (PH 7.0) WITH 0.1 M BETAINE MONOHYDRATE AS AN ADDITIVE. THE RATIOS OF PROTEIN (9.6 MG/ML) WITH BESTATIN (6 MM), RESERVOIR AND ADDITIVE IN THE DROPS WERE 2:1:0.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Details: RH-COATED SI MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→28.7 Å / Num. obs: 46277 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.31
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.25 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XPY

2xpy


Resolution: 1.955→28.66 Å / SU ML: 0.23 / σ(F): 0.03 / Phase error: 22.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 935 2 %
Rwork0.1897 --
obs0.1908 46277 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.947 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3914 Å2-0 Å2-0 Å2
2--0.7462 Å20 Å2
3----5.1377 Å2
Refinement stepCycle: LAST / Resolution: 1.955→28.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 27 350 5481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075273
X-RAY DIFFRACTIONf_angle_d1.1127153
X-RAY DIFFRACTIONf_dihedral_angle_d16.0891906
X-RAY DIFFRACTIONf_chiral_restr0.078772
X-RAY DIFFRACTIONf_plane_restr0.005921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9554-2.05840.27141170.21426008X-RAY DIFFRACTION90
2.0584-2.18730.27461450.20456564X-RAY DIFFRACTION98
2.1873-2.35620.3091180.20246339X-RAY DIFFRACTION94
2.3562-2.59310.25241250.20046310X-RAY DIFFRACTION94
2.5931-2.9680.2631500.19086460X-RAY DIFFRACTION95
2.968-3.73810.22581270.17466805X-RAY DIFFRACTION99
3.7381-28.66270.22421530.17556856X-RAY DIFFRACTION97
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)
10.5172-0.35370.26161.9615-1.24510.8244-0.131-0.1777-0.02040.5448-0.0534-0.06320.11510.16080.17930.1895-0.01620.01530.22230.01880.1209-13.8369-12.296330.3414
21.49410.5987-0.67691.2137-0.54011.3037-0.1323-0.0358-0.2372-0.042-0.06730.02620.35480.02170.11950.19840.02210.05520.09260.02930.1591-17.7317-22.577721.696
30.57890.4039-0.12782.1313-0.37581.0952-0.06150.01130.0974-0.2786-0.0726-0.03380.08930.20110.10630.11650.02670.04770.1510.03380.145-12.372-5.40635.8154
41.1255-0.4434-0.1521.7876-0.4470.6787-0.0151-0.08370.08920.29470.0020.1838-0.15210.01450.01670.1836-0.03230.02350.1133-0.02870.1531-22.40489.743423.1041
51.5799-2.50480.08543.0385-0.62940.84310.04050.0126-1.0523-0.50770.23971.65390.2411-0.1712-0.2810.1825-0.0198-0.14830.09120.12280.9044-42.63875.1145-0.5268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 40:104)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 105:198)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 199:337)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 338:511)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 512:671)

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