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- PDB-4gaa: Structure of Leukotriene A4 hydrolase from Xenopus laevis complex... -

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Basic information

Entry
Database: PDB / ID: 4gaa
TitleStructure of Leukotriene A4 hydrolase from Xenopus laevis complexed with inhibitor bestatin
ComponentsMGC78867 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Leukotriene A4 hydrolase / Metalloprotein / Hydrolase / protease / Zinc binding / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase / epoxide hydrolase activity / leukotriene biosynthetic process / peptide catabolic process / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding ...leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase / epoxide hydrolase activity / leukotriene biosynthetic process / peptide catabolic process / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / 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 / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / : / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / 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 / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / : / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / 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 / 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 / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsStsiapanava, A. / Kumar, R.B. / Haeggstrom, J.Z. / Rinaldo-Matthis, A.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Product formation controlled by substrate dynamics in leukotriene A4 hydrolase.
Authors: Stsiapanava, A. / Tholander, F. / Kumar, R.B. / Qureshi, A.A. / Niegowski, D. / Hasan, M. / Thunnissen, M. / Haeggstrom, J.Z. / Rinaldo-Matthis, A.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Feb 28, 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 / struct_conn / struct_site
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.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_asym_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_asym_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_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: MGC78867 protein
B: MGC78867 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,9466
Polymers138,1982
Non-polymers7484
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-79 kcal/mol
Surface area44950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.120, 52.170, 109.900
Angle α, β, γ (deg.)90.00, 111.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MGC78867 protein


Mass: 69099.047 Da / Num. of mol.: 2 / Fragment: Leukotriene A4 hydrolase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: lta4h, MGC78867 / Plasmid: PT3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: Q6IP81, leukotriene-A4 hydrolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BES / 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID / BESTATIN


Mass: 308.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24N2O4 / Comment: protease inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, 20 % PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2011 / Details: Toroidal mirror
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.26→29.304 Å / Num. all: 55359 / Num. obs: 54861 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 44.74 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.7
Reflection shellResolution: 2.261→2.268 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.9 / Num. unique all: 559 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.11.2refinement
PROCESSdata reduction
PROCESSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→29.3 Å / Cor.coef. Fo:Fc: 0.9311 / Cor.coef. Fo:Fc free: 0.9085 / SU R Cruickshank DPI: 0.416 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 2726 5.06 %RANDOM
Rwork0.2218 ---
all0.2232 55411 --
obs0.2232 53926 97.32 %-
Displacement parametersBiso mean: 89.94 Å2
Baniso -1Baniso -2Baniso -3
1-4.3764 Å20 Å2-3.5979 Å2
2---8.0758 Å20 Å2
3---3.6994 Å2
Refine analyzeLuzzati coordinate error obs: 0.595 Å
Refinement stepCycle: LAST / Resolution: 2.26→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9692 0 46 93 9831
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00910014HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0413601HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4608SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes228HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1432HARMONIC5
X-RAY DIFFRACTIONt_it10014HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion3.18
X-RAY DIFFRACTIONt_chiral_improper_torsion1296SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11546SEMIHARMONIC4
LS refinement shellResolution: 2.26→2.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2379 194 4.9 %
Rwork0.2227 3762 -
all0.2234 3956 -
obs--97.32 %
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)
13.0663-0.4019-2.74370.75480.60974.13970.4568-0.16191.09390.08580.4141-0.1561-0.21920.3564-0.8709-0.1316-0.00290.3657-0.6119-0.09420.1909-6.729525.839924.2827
213.39341.5022-5.42251.0167-0.48712.0288-0.33564.07180.5922-0.0670.61110.45580.0246-1.7068-0.2755-0.6222-0.11820.26060.30750.2632-0.2249-52.37099.224528.8305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|607 }A2 - 607
2X-RAY DIFFRACTION2{ B|2 - B|606 }B2 - 606

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