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- PDB-5hj9: Crystal structure of Leishmania mexicana arginase in complex with... -

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Basic information

Entry
Database: PDB / ID: 5hj9
TitleCrystal structure of Leishmania mexicana arginase in complex with inhibitor ABHPE
ComponentsArginase
KeywordsHYDROLASE
Function / homology
Function and homology information


arginine metabolic process / arginase / arginase activity / urea cycle / metal ion binding
Similarity search - Function
Ureohydrolase domain / Arginase / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / Chem-X7A / Arginase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsHai, Y. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 49758 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystal structures of Leishmania mexicana arginase complexed with alpha , alpha-disubstituted boronic amino-acid inhibitors.
Authors: Hai, Y. / Christianson, D.W.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 18, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_abbrev ..._chem_comp.name / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Revision 1.4Sep 27, 2023Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,12211
Polymers36,0341
Non-polymers1,08810
Water3,603200
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,36733
Polymers108,1033
Non-polymers3,26330
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)89.092, 89.092, 113.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Arginase


Mass: 36034.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Gene: ARG / Production host: Escherichia coli (E. coli) / References: UniProt: Q6TUJ5, arginase

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Non-polymers , 7 types, 210 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-X7A / [(5R)-5-amino-5-carboxy-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-)


Mass: 303.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28BN2O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 86060 / % possible obs: 99.3 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 29.3
Reflection shellHighest resolution: 1.28 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.51 / Rpim(I) all: 0.509 / Rsym value: 1.202 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
CBASSdata collection
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ITY

4ity


Resolution: 1.28→36.529 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.85 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1594 4338 5.04 %
Rwork0.1457 --
obs0.1507 86034 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.28→36.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 63 200 2620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012541
X-RAY DIFFRACTIONf_angle_d1.3023455
X-RAY DIFFRACTIONf_dihedral_angle_d14.4978
X-RAY DIFFRACTIONf_chiral_restr0.092400
X-RAY DIFFRACTIONf_plane_restr0.005440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2805-1.30250.36451850.3963756X-RAY DIFFRACTION87
1.3025-1.32620.29962060.35554036X-RAY DIFFRACTION93
1.3262-1.35170.30852330.30094063X-RAY DIFFRACTION95
1.3517-1.37920.27732130.26034083X-RAY DIFFRACTION95
1.3792-1.40920.25282280.23524124X-RAY DIFFRACTION95
1.4092-1.44190.23722330.22754118X-RAY DIFFRACTION95
1.4419-1.47790.22842270.21764042X-RAY DIFFRACTION95
1.4779-1.51780.24061880.20434171X-RAY DIFFRACTION96
1.5178-1.56240.21271530.20014129X-RAY DIFFRACTION96
1.5624-1.61270.20472080.20094132X-RAY DIFFRACTION95
1.6127-1.67020.2261780.1944151X-RAY DIFFRACTION96
1.6702-1.73690.2262210.19374115X-RAY DIFFRACTION95
1.7369-1.81570.20182000.19384121X-RAY DIFFRACTION95
1.8157-1.91110.17551900.18244113X-RAY DIFFRACTION96
1.9111-2.03040.17562130.17514156X-RAY DIFFRACTION95
2.0304-2.18640.17212570.16054047X-RAY DIFFRACTION94
2.1864-2.40490.15412020.15274109X-RAY DIFFRACTION95
2.4049-2.74970.15282710.14534056X-RAY DIFFRACTION94
2.7497-3.45190.1243080.11874020X-RAY DIFFRACTION93
3.4519-12.41870.12382150.07754062X-RAY DIFFRACTION94

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