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

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Basic information

Entry
Database: PDB / ID: 5hja
TitleCrystal structure of Leishmania mexicana arginase in complex with inhibitor ABHDP
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
: / Chem-XA2 / Arginase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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)36,6715
Polymers36,0341
Non-polymers6364
Water2,630146
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,01215
Polymers108,1033
Non-polymers1,90812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5570 Å2
ΔGint-19 kcal/mol
Surface area31680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.934, 88.934, 113.867
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 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
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-XA2 / (R)-2-amino-6-borono-2-(1-(3,4-dichlorobenzyl)piperidin-4-yl)hexanoic acid


Mass: 434.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H28BCl2N2O5
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.4 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.2, 22% 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: Apr 23, 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: 1.65→50 Å / Num. obs: 40479 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 22.4
Reflection shellHighest resolution: 1.65 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.817 / Rpim(I) all: 0.316 / Rsym value: 0.73 / % possible all: 95.3

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Processing

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

4ity


Resolution: 1.65→45.783 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.97 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2125 2019 5.01 %
Rwork0.1873 --
obs0.189 40270 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→45.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 36 146 2494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032404
X-RAY DIFFRACTIONf_angle_d0.8063262
X-RAY DIFFRACTIONf_dihedral_angle_d14.693906
X-RAY DIFFRACTIONf_chiral_restr0.028373
X-RAY DIFFRACTIONf_plane_restr0.003419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.651-1.69230.30811370.3092620X-RAY DIFFRACTION90
1.6923-1.7380.29171270.29042762X-RAY DIFFRACTION95
1.738-1.78910.34311400.26952749X-RAY DIFFRACTION95
1.7891-1.84690.28761350.25362712X-RAY DIFFRACTION95
1.8469-1.91280.24681360.23742747X-RAY DIFFRACTION95
1.9128-1.98940.26551380.2382771X-RAY DIFFRACTION95
1.9894-2.07980.24661390.23152718X-RAY DIFFRACTION95
2.0798-2.18940.24771650.21682728X-RAY DIFFRACTION94
2.1894-2.32640.21491350.20842741X-RAY DIFFRACTION95
2.3264-2.50580.23851360.20332724X-RAY DIFFRACTION95
2.5058-2.75760.20821620.19452738X-RAY DIFFRACTION94
2.7576-3.15570.22711510.18842736X-RAY DIFFRACTION95
3.1557-3.97210.1861550.15242723X-RAY DIFFRACTION95
3.9721-22.23550.17161600.14492726X-RAY DIFFRACTION94
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)
10.0880.0490.02490.09530.14870.1047-0.07990.1547-0.5329-0.1870.0992-0.028-0.05180.044-00.2657-0.0168-0.01980.1666-0.07660.1739-17.5007-23.30529.4439
2-0.0121-0.03420.0171-0.01780.0111-0.0046-0.34120.19310.0865-0.2863-0.08420.04510.1147-0.151-0-0.1224-0.1009-0.8360.3836-0.1047-0.4037-34.4559-10.260321.3672
3-0.00710.00290.01070.0008-0.0166-0.0183-0.2646-0.0385-0.2481-0.0959-0.05660.20010.1283-0.0495-00.1503-0.0491-0.0410.1521-0.02520.2939-32.4336-21.421734.3578
40.2555-0.07630.14750.43060.03160.0545-0.0539-0.08640.0484-0.0859-0.00090.17470.0042-0.006200.1133-0.0055-0.02180.129-0.01770.1199-24.3801-8.217542.5403
5-0.0059-0.00050.0051-0.0074-0.00590.0001-0.02620.18980.1026-0.0832-0.03070.0017-0.1033-0.1327-00.2175-0.03040.04790.237-0.00810.1399-10.5667-2.826530.4288
6-0.00460.0620.00510.07210.04310.0092-0.09910.0008-0.1838-0.13710.0481-0.29240.0256-0.053900.1635-0.0192-0.00150.1411-0.01570.1201-11.0405-13.858738.4547
7-0.0096-0.00810.0308-0.00630.0139-0.0052-0.0872-0.1373-0.1614-0.1014-0.0845-0.1758-0.0366-0.057100.1547-0.01650.03920.1317-0.03940.2458-5.1206-18.99536.9815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 82 )
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 102 )
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 246 )
5X-RAY DIFFRACTION5chain 'A' and (resid 247 through 264 )
6X-RAY DIFFRACTION6chain 'A' and (resid 265 through 301 )
7X-RAY DIFFRACTION7chain 'A' and (resid 302 through 322 )

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