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- PDB-4ie1: Crystal structure of human Arginase-1 complexed with inhibitor 1h -

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Basic information

Entry
Database: PDB / ID: 4ie1
TitleCrystal structure of human Arginase-1 complexed with inhibitor 1h
ComponentsArginase-1
KeywordsHydrolase/Hydrolase inhibitor / Boron compounds / 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 / arginine catabolic process to ornithine / arginase / 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 / arginine catabolic process to ornithine / arginase / 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-1EC / : / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.0006 Å
AuthorsCousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Beckett, P. / Van Zandt, M.C. / Ji, M.K. / Whitehouse, D. / Ryder, T. / Jagdmann, E. / Andreoli, M. ...Cousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Beckett, P. / Van Zandt, M.C. / Ji, M.K. / Whitehouse, D. / Ryder, T. / Jagdmann, E. / Andreoli, M. / Mazur, A. / Padmanilayam, M. / Schroeter, H. / Golebiowski, A. / Podjarny, A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: 2-Substituted-2-amino-6-boronohexanoic acids as arginase inhibitors.
Authors: Golebiowski, A. / Paul Beckett, R. / Van Zandt, M. / Ji, M.K. / Whitehouse, D. / Ryder, T.R. / Jagdmann, E. / Andreoli, M. / Mazur, A. / Padmanilayam, M. / Cousido-Siah, A. / Mitschler, A. / ...Authors: Golebiowski, A. / Paul Beckett, R. / Van Zandt, M. / Ji, M.K. / Whitehouse, D. / Ryder, T.R. / Jagdmann, E. / Andreoli, M. / Mazur, A. / Padmanilayam, M. / Cousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Podjarny, A. / Schroeter, H.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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

Downloads & links

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Assembly

Deposited unit
A: Arginase-1
B: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5688
Polymers67,8482
Non-polymers7206
Water3,405189
1
A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,85112
Polymers101,7723
Non-polymers1,0809
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area5600 Å2
ΔGint-15 kcal/mol
Surface area32780 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)102,85112
Polymers101,7723
Non-polymers1,0809
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 area5440 Å2
ΔGint-13 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.074, 90.074, 69.272
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
11A-587-

HOH

21B-623-

HOH

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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-1EC / [(5R)-5-amino-5-carboxy-8-hydroxyoctyl](trihydroxy)borate(1-)


Mass: 250.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H21BNO6
#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 / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 17, 2008 / Details: OSMIC MIRRORS
RadiationMonochromator: DOUBLE MIRRORS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.02
ReflectionResolution: 2→50 Å / Num. all: 42561 / Num. obs: 41127 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.076 / Χ2: 1.067 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.071.90.2739061.064192.5
2.07-2.151.90.22639701.084192.7
2.15-2.251.90.1939501.081193.4
2.25-2.371.90.16340181.095193.7
2.37-2.521.90.1439831.088194.5
2.52-2.711.90.11340491.085195
2.71-2.991.90.09740761.04195.4
2.99-3.421.90.06840511.067196
3.42-4.311.90.05140921.047196.1
4.31-501.90.03941061.025196.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1d3v


Resolution: 2.0006→21.635 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.9509 / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Phase error: 10.14 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.127 2079 5.06 %Random 5%
Rwork0.1061 ---
all0.1079 41127 --
obs0.1079 41127 96.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.5 Å2 / Biso mean: 21.4664 Å2 / Biso min: 8.45 Å2
Refinement stepCycle: LAST / Resolution: 2.0006→21.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 38 189 5001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144915
X-RAY DIFFRACTIONf_angle_d1.746671
X-RAY DIFFRACTIONf_chiral_restr0.141767
X-RAY DIFFRACTIONf_plane_restr0.009856
X-RAY DIFFRACTIONf_dihedral_angle_d15.6051845
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0006-2.04710.07891110.06792536264790
2.0471-2.09820.09481690.07092533270289
2.0982-2.15480.0831470.08222541268891
2.1548-2.21810.09991350.08112566270191
2.2181-2.28960.12351290.08332575270491
2.2896-2.37120.11711260.09092623274992
2.3712-2.46590.13451370.09812560269791
2.4659-2.57780.11921400.09782622276292
2.5778-2.71320.13261290.10782624275393
2.7132-2.88240.16111480.11862576272492
2.8824-3.10380.13411500.11432647279793
3.1038-3.4140.15631530.1252591274492
3.414-3.9030.14161290.12012664279394
3.903-4.89870.10881510.09672628277993
4.8987-17.26620.15281250.13272681280695

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