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- PDB-4hxq: Crystal structure of human Arginase-1 complexed with inhibitor 14 -

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Basic information

Entry
Database: PDB / ID: 4hxq
TitleCrystal structure of human Arginase-1 complexed with inhibitor 14
ComponentsArginase-1
KeywordsHydrolase/Hydrolase Inhibitor / metalloenzyme / alpha/beta fold / Hydrolase / Arginine metabolism / Manganese / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation ...positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation / arginine catabolic process / negative regulation of T cell proliferation / specific granule lumen / azurophil granule lumen / manganese ion binding / adaptive immune response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleus / cytosol / cytoplasm
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-X8A / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsCousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Whitehouse, D.L. / Golebiowski, A. / Ji, M. / Zhang, M. / Beckett, P. / Sheeler, R. / Andreoli, M. ...Cousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Whitehouse, D.L. / Golebiowski, A. / Ji, M. / Zhang, M. / Beckett, P. / Sheeler, R. / Andreoli, M. / Conway, B. / Mahboubi, K. / Schroeter, H. / Van Zandt, M.C. / Podjarny, A.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Discovery of (R)-2-Amino-6-borono-2-(2-(piperidin-1-yl)ethyl)hexanoic Acid and Congeners As Highly Potent Inhibitors of Human Arginases I and II for Treatment of Myocardial Reperfusion Injury.
Authors: Van Zandt, M.C. / Whitehouse, D.L. / Golebiowski, A. / Ji, M.K. / Zhang, M. / Beckett, R.P. / Jagdmann, G.E. / Ryder, T.R. / Sheeler, R. / Andreoli, M. / Conway, B. / Mahboubi, K. / ...Authors: Van Zandt, M.C. / Whitehouse, D.L. / Golebiowski, A. / Ji, M.K. / Zhang, M. / Beckett, R.P. / Jagdmann, G.E. / Ryder, T.R. / Sheeler, R. / Andreoli, M. / Conway, B. / Mahboubi, K. / D'Angelo, G. / Mitschler, A. / Cousido-Siah, A. / Ruiz, F.X. / Howard, E.I. / Podjarny, A.D. / Schroeter, H.
History
DepositionNov 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.5Sep 20, 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 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_seq_id / _struct_conn.ptnr2_label_asym_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: Arginase-1
B: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7028
Polymers67,8482
Non-polymers8546
Water8,107450
1
A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,05312
Polymers101,7723
Non-polymers1,2819
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area5590 Å2
ΔGint-19 kcal/mol
Surface area33190 Å2
MethodPISA
2
B: Arginase-1
hetero molecules

B: Arginase-1
hetero molecules

B: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,05312
Polymers101,7723
Non-polymers1,2819
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 area5480 Å2
ΔGint-19 kcal/mol
Surface area33270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.321, 90.321, 69.534
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11B-627-

HOH

21B-654-

HOH

Detailsbiological assembly is a trimer generated from monomer A in the asymmetric unit by the operations: -x+y, -x, z-l; -y, x-y, z+1; or from monomer B in the asymmetric unit by the operations: -x+y, -x, z; -y, x-y, z

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Components

#1: Protein Arginase-1 / Liver-type arginase / Type I arginase


Mass: 33923.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05089, arginase
#2: Chemical ChemComp-X8A / [(5R)-5-carboxy-5-(methylamino)-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-)


Mass: 317.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30BN2O5
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Malonic Acid, Imidazol, Boric system, 25% Polyethylene Glycol (PEG) 1500, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.70849 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2012
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70849 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 1.45→50 Å / Num. all: 111989 / Num. obs: 111989 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.053 / Χ2: 1.036 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.45-1.54.10.469110701.008198.5
1.5-1.564.60.376112141.041199.1
1.56-1.6350.303110951.051199.2
1.63-1.725.10.242112141.06199.4
1.72-1.8350.179111851.074199.4
1.83-1.974.80.11112341.056199.7
1.97-2.175.20.075112301.029199.7
2.17-2.484.90.053112471.008199.8
2.48-3.125.20.038112421.004199.9
3.12-5050.028112581.029199.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1D3V

1d3v


Resolution: 1.45→39.11 Å / Occupancy max: 1 / Occupancy min: 0.55 / Cross valid method: R-free / σ(F): 0 / Phase error: 18.33 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 5614 5.01 %Random 5%
Rwork0.188 ---
all0.1941 111988 --
obs0.1941 111988 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 25.94 Å2 / Biso mean: 9.656 Å2 / Biso min: 4.1 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 48 450 5272
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.347
X-RAY DIFFRACTIONf_chiral_restr0.12
X-RAY DIFFRACTIONf_plane_restr0.007
X-RAY DIFFRACTIONf_dihedral_angle_d15.645
LS refinement shellResolution: 1.4496→1.4746 Å
RfactorNum. reflection% reflection
Rfree0.3692 286 -
Rwork0.3135 --
obs-5215 93 %

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