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- PDB-2aeb: Crystal structure of human arginase I at 1.29 A resolution and ex... -

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Basic information

Entry
Database: PDB / ID: 2aeb
TitleCrystal structure of human arginase I at 1.29 A resolution and exploration of inhibition in immune response.
ComponentsArginase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / BINUCLEAR MANGANESE CLUSTER / BORONIC ACID INHIBITOR / PERFECTLY TWINNED CRYSTAL / 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
2(S)-AMINO-6-BORONOHEXANOIC ACID / : / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.29 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.
#2: Journal: Nat.Struct.Biol. / Year: 1999
Title: Arginase-Boronic Acid Complex Highlights a Physiological Role in Erectile Function
Authors: Cox, J.D. / Kim, N.N. / Traish, A.M. / Christianson, D.W.
History
DepositionJul 21, 2005Deposition site: RCSB / Processing site: RCSB
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 1.3Jul 27, 2011Group: Version format compliance
Revision 1.4Apr 3, 2013Group: Other
Revision 1.5Mar 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.6Aug 23, 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_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 / _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)70,1648
Polymers69,5602
Non-polymers6046
Water6,918384
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_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
2
B: Arginase 1
hetero molecules

B: Arginase 1
hetero molecules

B: Arginase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24512
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
Unit cell
Length a, b, c (Å)91.422, 91.422, 69.637
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-2518-

HOH

21B-1523-

HOH

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Components

#1: Protein Arginase 1 / 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) / 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


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.41 Å3/Da / Density % sol: 49.04 % / Description: DATA WERE SCALED AS SG P3.
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: PegMME 5000, Bis Tris, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 294.0K, pH 7.10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9124
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9124 Å / Relative weight: 1
ReflectionResolution: 1.29→50 Å / Num. obs: 150499 / % possible obs: 92.7 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.6
Reflection shellResolution: 1.29→1.34 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.85 / % possible all: 86

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
SHELXL-97refinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1D3V

1d3v


Highest resolution: 1.29 Å
Details: DUE TO POORLY DEFINED DENSITY, THE FOLLOWING RESIDUES: A5, A48 (NZ), A222 (SIDE CHAINS), B41 (SIDE CHAINS), B48 (SIDE CHAINS), B89 (NZ), B222 (SIDE CHAINS) AND B224 (SIDE CHAINS) HAVE BEEN ...Details: DUE TO POORLY DEFINED DENSITY, THE FOLLOWING RESIDUES: A5, A48 (NZ), A222 (SIDE CHAINS), B41 (SIDE CHAINS), B48 (SIDE CHAINS), B89 (NZ), B222 (SIDE CHAINS) AND B224 (SIDE CHAINS) HAVE BEEN MODELED AT MINOR OCCUPANCY. BECAUSE PART OF A DISORDERED SIDE CHAINS, RESIDUES A83 AND B217 HAVE DISORDERED DENSITY. THEREFORE, HYDROGENS ARE NOT PLACED IN THE SIDECHAINS OF THESE TWO RESIDUE. REFINED TWIN FRACTIONS: 0.46. TWIN OPERATOR: -H, -K, L
RfactorNum. reflection
Rfree0.152 7526
all-150499
Refinement stepCycle: LAST / Highest resolution: 1.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4731 0 30 384 5145
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.03
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d2.79
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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