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- PDB-2pll: Crystal structure of perdeuterated human arginase I -

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Basic information

Entry
Database: PDB / ID: 2pll
TitleCrystal structure of perdeuterated human arginase I
Componentsarginase-1
KeywordsHYDROLASE / Perdeuterated protein / X-ray structure
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
2(S)-AMINO-6-BORONOHEXANOIC ACID / : / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDi Costanzo, L. / Moulin, M. / Haertlein, M. / Meilleur, F. / Christianson, D.W.
CitationJournal: Arch.Biochem.Biophys. / Year: 2007
Title: Expression, purification, assay, and crystal structure of perdeuterated human arginase I
Authors: Di Costanzo, L. / Moulin, M. / Haertlein, M. / Meilleur, F. / Christianson, D.W.
History
DepositionApr 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jul 28, 2021Group: Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine ...pdbx_struct_conn_angle / refine / struct_conn / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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 / _refine.ls_percent_reflns_obs / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)70,1648
Polymers69,5602
Non-polymers6046
Water6,467359
1
A: arginase-1
hetero molecules

A: arginase-1
hetero molecules

A: arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24512
Polymers104,3403
Non-polymers9069
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7970 Å2
ΔGint-50 kcal/mol
Surface area32470 Å2
MethodPISA, PQS
2
B: arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0824
Polymers34,7801
Non-polymers3023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: arginase-1
hetero molecules

B: arginase-1
hetero molecules

B: arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24512
Polymers104,3403
Non-polymers9069
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)90.784, 90.784, 69.514
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 / / E.C.3.5.3.1 / 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 / Plasmid: pET-24a / 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-ABH / 2(S)-AMINO-6-BORONOHEXANOIC ACID


Mass: 191.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15BNO5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1 M Bis-Tris (pH 5.5), 10-20% (wt/vol) Peg-3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→69.5 Å / Num. obs: 46244 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Redundancy: 1.4 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.6862 / Mean I/σ(I) obs: 2 / % possible all: 93.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AEB: monomer A

2aeb


Resolution: 1.9→69.5 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1908 -Random
Rwork0.141 ---
all-46244 --
obs-42382 91.6 %-
Refinement stepCycle: LAST / Resolution: 1.9→69.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 30 359 5163
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angles_deg22.6
LS refinement shellResolution: 1.8→1.9 Å / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.235

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