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- PDB-1wva: Crystal structure of human arginase I from twinned crystal -

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Basic information

Entry
Database: PDB / ID: 1wva
TitleCrystal structure of human arginase I from twinned crystal
ComponentsArginase 1
KeywordsHYDROLASE / twinned crystal / BEC inhibitor
Function / homology
Function and homology information


positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / Urea cycle / arginase / arginase activity / : / urea cycle / response to nematode / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan ...positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / Urea cycle / arginase / arginase activity / : / urea cycle / response to nematode / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / 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 / cytosol / cytoplasm
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
: / S-2-(BORONOETHYL)-L-CYSTEINE / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsDi Costanzo, L. / Sabio, G. / Mora, A. / Rodriguez, P.C. / Ochoa, A.C. / Centeno, F. / Christianson, D.W.
Citation
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.
#1: Journal: Biochemistry / Year: 2003
Title: Human arginase II: crystal structure and physiological role in male and female sexual arousal
Authors: Cama, E. / Colleluori, D.M. / Emig, F.A. / Shin, H. / Kim, S.W. / Kim, N.N. / Traish, A.M. / Ash, D.E. / Christianson, D.W.
History
DepositionDec 14, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn.ptnr2_label_seq_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,2008
Polymers69,5602
Non-polymers6406
Water3,621201
1
A: Arginase 1
hetero molecules

A: Arginase 1
hetero molecules

A: Arginase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,29912
Polymers104,3403
Non-polymers9609
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
B: Arginase 1
hetero molecules

B: Arginase 1
hetero molecules

B: Arginase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,29912
Polymers104,3403
Non-polymers9609
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
Unit cell
Length a, b, c (Å)90.602, 90.602, 69.311
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
11B-1388-

HOH

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Components

#1: Protein Arginase 1 / arginase I / 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) / Plasmid: pET11-d / 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-S2C / S-2-(BORONOETHYL)-L-CYSTEINE


Type: L-peptide linking / Mass: 210.036 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13BNO5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEGMME 5000, bis-tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 46041 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 8.7
Reflection shellResolution: 1.94→2.02 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / Num. unique all: 2121 / Rsym value: 0.34 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALAdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D3V

1d3v


Resolution: 1.94→50 Å / σ(F): 1 / σ(I): 1
Details: This is a twinned structure. The twinning operator is (h,k,l) -> (-h,-k,l) and the twinning fraction is 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 4119 -RANDOM
Rwork0.1504 ---
obs0.1504 45844 98.8 %-
Refinement stepCycle: LAST / Resolution: 1.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4688 0 30 201 4919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.9

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