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- PDB-3kv2: HIGH RESOLUTION STRUCTURE OF HUMAN ARGINASE I IN COMPLEX WITH THE... -

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Basic information

Entry
Database: PDB / ID: 3kv2
TitleHIGH RESOLUTION STRUCTURE OF HUMAN ARGINASE I IN COMPLEX WITH THE STRONG INHIBITOR N(omega)-hydroxy-nor-L-arginine (nor-NOHA)
ComponentsArginase-1
KeywordsHYDROLASE / STRONG INHIBITOR / nor-NOHA / ARGINASE / HIGH RESOLUTION / Alternative splicing / Arginine metabolism / Cytoplasm / Disease mutation / Manganese / Metal-binding / Phosphoprotein / Polymorphism / Urea cycle
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
: / NOR-N-OMEGA-HYDROXY-L-ARGININE / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 1.55 Å
AuthorsDi Costanzo, L. / Christianson, D.W.
CitationJournal: Arch.Biochem.Biophys. / Year: 2010
Title: Inhibition of human arginase I by substrate and product analogues.
Authors: Di Costanzo, L. / Ilies, M. / Thorn, K.J. / Christianson, D.W.
History
DepositionNov 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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

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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)70,1328
Polymers69,5602
Non-polymers5726
Water5,441302
1
A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,19812
Polymers104,3403
Non-polymers8589
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 area5580 Å2
ΔGint-21 kcal/mol
Surface area32480 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)105,19812
Polymers104,3403
Non-polymers8589
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 area5490 Å2
ΔGint-17 kcal/mol
Surface area32000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.497, 90.497, 69.604
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Arginase-1 / Type I arginase / Liver-type 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 / Production host: Escherichia coli (E. coli) / 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-NNH / NOR-N-OMEGA-HYDROXY-L-ARGININE


Type: L-peptide linking / Mass: 176.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growMethod: vapor diffusion, hanging drop
Details: Hanging drops containing 3 L protein solution [3.5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM nor-NOHA, 100 M MnCl2] and 3 L precipitant solution [0.1 M bis-Tris (pH 6.5), 28% PEG monomethyl ...Details: Hanging drops containing 3 L protein solution [3.5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM nor-NOHA, 100 M MnCl2] and 3 L precipitant solution [0.1 M bis-Tris (pH 6.5), 28% PEG monomethyl ether 2000] were equilibrated over a 1 mL reservoir of precipitant solution at 2 C. , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 90987 / Num. obs: 90987 / % possible obs: 98.2 % / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 14.4
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 2 % / Rmerge(I) obs: 0.302 / % possible all: 96.2

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: PHASER
Starting model: 2ZAV monomer A

2zav


Resolution: 1.55→50 Å
Details: Data in the structure factor file is twinned. The operator is -h,-k,l, and the fraction is 0.5
RfactorNum. reflection% reflection
Rfree0.1782 4185 -
Rwork0.1436 --
all0.1436 85281 -
obs0.1436 85281 92 %
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4762 0 28 302 5092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 1.55→1.61 Å /
RfactorNum. reflection
Rwork0.2241 -
Rfree-0

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