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- PDB-3skk: Crystal structure of human arginase I in complex with the inhibit... -

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Basic information

Entry
Database: PDB / ID: 3skk
TitleCrystal structure of human arginase I in complex with the inhibitor FABH, Resolution 1.70 A, twinned structure
ComponentsArginase-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ABH inhibitor derivative / twinning / 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 / arginase activity / : / urea cycle / response to nematode / defense response to protozoan / negative regulation of type II interferon-mediated signaling pathway ...positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / : / urea cycle / response to nematode / defense response to protozoan / negative regulation of type II interferon-mediated signaling pathway / negative regulation of activated T cell proliferation / L-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 / cytoplasm / cytosol
Similarity search - Function
Arginase / Ureohydrolase domain / 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-4U7 / : / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsThorn, K.J. / Di Costanzo, L. / Christianson, D.W.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Binding of alpha , alpha-disubstituted amino acids to arginase suggests new avenues for inhibitor design.
Authors: Ilies, M. / Di Costanzo, L. / Dowling, D.P. / Thorn, K.J. / Christianson, D.W.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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_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
Revision 1.2Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)70,2648
Polymers69,5602
Non-polymers7046
Water13,691760
1
A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,39512
Polymers104,3403
Non-polymers1,0569
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5620 Å2
ΔGint-17 kcal/mol
Surface area32570 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)105,39512
Polymers104,3403
Non-polymers1,0569
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 area5580 Å2
ΔGint-15 kcal/mol
Surface area32650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.094, 90.094, 69.362
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

21A-446-

HOH

31A-485-

HOH

41A-532-

HOH

51A-616-

HOH

61A-692-

HOH

71B-442-

HOH

81B-720-

HOH

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Components

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


Mass: 34779.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Plasmid: pet11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P05089, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-4U7 / [(5S)-5-amino-5-carboxy-6,6-difluorohexyl](trihydroxy)borate(1-)


Type: L-peptide linking / Mass: 242.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15BF2NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STARTING MATERIAL 2-AMINO-6-BORONO-2-(DIFLUOROMETHYL)HEXANOIC ACID (FABH) UNDERGOES TO ...THE STARTING MATERIAL 2-AMINO-6-BORONO-2-(DIFLUOROMETHYL)HEXANOIC ACID (FABH) UNDERGOES TO NUCLEOPHILIC ATTACK BY THE HYDROXYL GROUP BRIDGING THE DI-MANGANESE CLUSTER OF THE ENZYME.

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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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 3 uL of protein solution [3.5 mg/mL HAI, 50 mM bicine (pH 8.5), 2 mM FABH, 100 M MnCl2] and 3 uL of precipitant solution [0.1 M HEPES (pH 7.0), 22-28% Jeffamine] were equilibrated against a ...Details: 3 uL of protein solution [3.5 mg/mL HAI, 50 mM bicine (pH 8.5), 2 mM FABH, 100 M MnCl2] and 3 uL of precipitant solution [0.1 M HEPES (pH 7.0), 22-28% Jeffamine] were equilibrated against a 1 mL reservoir of precipitant solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 1.7→50 Å / Num. all: 66860 / Num. obs: 66860 / % possible obs: 99 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 11.6
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.3 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZAV

2zav


Resolution: 1.701→37.779 Å / σ(F): 0.13 / Phase error: 24.55 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1779 6632 9.92 %
Rwork0.136 --
obs0.1401 66860 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.417 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1477 Å2-0 Å20 Å2
2---0.1477 Å2-0 Å2
3---0.2954 Å2
Refinement stepCycle: LAST / Resolution: 1.701→37.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 0 36 760 5574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064908
X-RAY DIFFRACTIONf_angle_d1.0436664
X-RAY DIFFRACTIONf_dihedral_angle_d17.591816
X-RAY DIFFRACTIONf_chiral_restr0.065764
X-RAY DIFFRACTIONf_plane_restr0.005856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7014-1.73070.23442920.21092701X-RAY DIFFRACTION79
1.7307-1.76220.26032800.20762808X-RAY DIFFRACTION82
1.7622-1.79610.22482920.20032864X-RAY DIFFRACTION82
1.7961-1.83270.20783550.19252855X-RAY DIFFRACTION83
1.8327-1.87260.20343170.18832974X-RAY DIFFRACTION85
1.8726-1.91610.19643070.17483007X-RAY DIFFRACTION87
1.9161-1.9640.21473340.16993007X-RAY DIFFRACTION87
1.964-2.01710.18623390.16992989X-RAY DIFFRACTION87
2.0171-2.07640.19623310.15753064X-RAY DIFFRACTION88
2.0764-2.14340.20323890.15563010X-RAY DIFFRACTION87
2.1434-2.220.20952990.15253099X-RAY DIFFRACTION90
2.22-2.30880.18642700.14883144X-RAY DIFFRACTION91
2.3088-2.41390.17663230.14983090X-RAY DIFFRACTION89
2.4139-2.5410.20023590.14993063X-RAY DIFFRACTION89
2.541-2.70010.19613610.14143094X-RAY DIFFRACTION89
2.7001-2.90840.15863460.13823109X-RAY DIFFRACTION90
2.9084-3.20060.18123290.12033065X-RAY DIFFRACTION90
3.2006-3.66280.15893500.10123124X-RAY DIFFRACTION90
3.6628-4.61110.13213460.08143103X-RAY DIFFRACTION90
4.6111-27.14260.14943100.09613141X-RAY DIFFRACTION91

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