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

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Basic information

Entry
Database: PDB / ID: 3sjt
TitleCrystal structure of human arginase I in complex with the inhibitor Me-ABH, Resolution 1.60 A, twinned structure
ComponentsArginase-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydrolase / ABH inhibitor derivative / twinning / 2-Amino-6-borono-2-methylhexanoic acid / 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
[(5S)-5-amino-5-carboxyhexyl](trihydroxy)borate / : / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.597 Å
AuthorsDi Costanzo, L. / Christianson, D.W.
Citation
Journal: 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.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Crystal structure of human arginase I at 1.29-A resolution and exploration of inhibition in the immune response.
Authors: Di Costanzo, L. / Sabio, G. / Mora, A. / Rodriguez, P.C. / Ochoa, A.C. / Centeno, F. / Christianson, D.W.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Atomic model
Revision 1.2Jul 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 1.3Sep 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)70,1928
Polymers69,5602
Non-polymers6326
Water13,781765
1
A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,28712
Polymers104,3403
Non-polymers9489
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 area5610 Å2
ΔGint-18 kcal/mol
Surface area32500 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)105,28712
Polymers104,3403
Non-polymers9489
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 area5510 Å2
ΔGint-17 kcal/mol
Surface area32500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.337, 90.337, 69.329
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-345-

HOH

21A-436-

HOH

31B-350-

HOH

41B-352-

HOH

51B-497-

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: pet-11d / 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-5AB / [(5S)-5-amino-5-carboxyhexyl](trihydroxy)borate


Type: L-peptide linking / Mass: 206.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17BNO5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 765 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STARTING MATERIAL 2-AMINO-6-BORONO-2-METHYLHEXANOIC ACID (MABH) UNDERGOES TO NUCLEOPHILIC ...THE STARTING MATERIAL 2-AMINO-6-BORONO-2-METHYLHEXANOIC ACID (MABH) UNDERGOES TO NUCLEOPHILIC ATTACK BY THE HYDROXYL GROUP BRIDING 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: 2.35 Å3/Da / Density % sol: 47.61 %
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 MABH, 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 MABH, 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: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2008
RadiationMonochromator: Double crystal cryo-cooled / Protocol: 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: 1.597→50 Å / Num. obs: 82598 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.1
Reflection shellResolution: 1.597→1.7 Å / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.7 / % possible all: 95.6

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Processing

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

2zav


Resolution: 1.597→34.068 Å / σ(F): 0.09 / Phase error: 17.86 / Stereochemistry target values: TWIN_LSQ_F / Details: twinning fraction = 0.5 twin law = -h, -k, l
RfactorNum. reflection% reflection
Rfree0.1631 2039 2.51 %
Rwork0.1292 --
obs0.1301 81125 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.135 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0703 Å2-0 Å2-0 Å2
2--1.0703 Å20 Å2
3----2.1405 Å2
Refinement stepCycle: LAST / Resolution: 1.597→34.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4762 0 32 765 5559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064888
X-RAY DIFFRACTIONf_angle_d1.046636
X-RAY DIFFRACTIONf_dihedral_angle_d17.5991828
X-RAY DIFFRACTIONf_chiral_restr0.066760
X-RAY DIFFRACTIONf_plane_restr0.005850
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5985-1.63850.25181390.23955121526086
1.6385-1.68280.22461340.22635291542588
1.6828-1.73230.25941350.21665440557591
1.7323-1.78820.20541310.2075542567393
1.7882-1.85210.21941430.19095661580495
1.8521-1.92620.22661410.17565768590996
1.9262-2.01390.18241430.17665776591997
2.0139-2.120.1621540.15755823597797
2.12-2.25280.17851520.15255790594297
2.2528-2.42670.14521480.14455852600097
2.4267-2.67070.18671440.13585853599798
2.6707-3.05690.16611410.11785802594397
3.0569-3.850.13781390.0865765590496
3.85-29.57480.11371350.07555530566592

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