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- PDB-1pq3: Human Arginase II: Crystal Structure and Physiological Role in Ma... -

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Basic information

Entry
Database: PDB / ID: 1pq3
TitleHuman Arginase II: Crystal Structure and Physiological Role in Male and Female Sexual Arousal
ComponentsArginase II, mitochondrial precursor
KeywordsHYDROLASE / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


negative regulation of chemokine (C-C motif) ligand 4 production / negative regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of defense response to bacterium / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of type 2 immune response / negative regulation of chemokine (C-C motif) ligand 5 production / negative regulation of interleukin-13 production / regulation of interleukin-1 beta production / Urea cycle / arginine catabolic process to ornithine ...negative regulation of chemokine (C-C motif) ligand 4 production / negative regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of defense response to bacterium / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of type 2 immune response / negative regulation of chemokine (C-C motif) ligand 5 production / negative regulation of interleukin-13 production / regulation of interleukin-1 beta production / Urea cycle / arginine catabolic process to ornithine / arginase / arginase activity / urea cycle / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of interleukin-17 production / regulation of reactive oxygen species biosynthetic process / ureteric bud development / negative regulation of tumor necrosis factor production / striated muscle contraction / nitric oxide biosynthetic process / positive regulation of cellular senescence / manganese ion binding / adaptive immune response / mitochondrial matrix / innate immune response / mitochondrion / 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
: / S-2-(BORONOETHYL)-L-CYSTEINE / Arginase-2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCama, E. / Colleluori, D.M. / Emig, F.A. / Shin, H. / Kim, S.W. / Kim, N.N. / Traish, A.M. / Ash, D.E. / Christianson, D.W.
CitationJournal: 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
DepositionJun 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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

Downloads & links

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Assembly

Deposited unit
A: Arginase II, mitochondrial precursor
B: Arginase II, mitochondrial precursor
C: Arginase II, mitochondrial precursor
D: Arginase II, mitochondrial precursor
E: Arginase II, mitochondrial precursor
F: Arginase II, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,92844
Polymers199,3906
Non-polymers3,53838
Water7,332407
1
A: Arginase II, mitochondrial precursor
B: Arginase II, mitochondrial precursor
C: Arginase II, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,39821
Polymers99,6953
Non-polymers1,70318
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Arginase II, mitochondrial precursor
E: Arginase II, mitochondrial precursor
F: Arginase II, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,53023
Polymers99,6953
Non-polymers1,83520
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.994, 142.994, 127.328
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Arginase II, mitochondrial precursor / / Non-hepatic arginase / Kidney-type arginase


Mass: 33231.656 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P78540, arginase

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Non-polymers , 5 types, 445 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-S2C / S-2-(BORONOETHYL)-L-CYSTEINE


Type: L-peptide linking / Mass: 210.036 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H13BNO5S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 3.77 Å3/Da / Density % sol: 67.35 %
Crystal growTemperature: 277 K / pH: 8.5
Details: Tris, Ammonium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 8.50
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlarginase1drop
25 mMBEC1drop
350 mMBicine1droppH8.5
40.10 MTris-HCl1droppH8.3-8.5
53.0 Mammonium sulfate1drop
60.10 MTris-HCl1reservoirpH8.3-8.5
73.0 Mammonium sulfate1reservoir
820 %(v/v)glycerol1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.916
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: RH-COATED SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 79653 / Num. obs: 75977
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 79653 / % possible obs: 99.3 % / Num. measured all: 404391 / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 98.9 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / σ(F): 0
RfactorNum. reflection
Rfree0.247 3837
Rwork0.227 -
obs0.227 75977
all-79653
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14022 0 170 407 14599
LS refinement shellResolution: 2.7→2.87 Å
RfactorNum. reflection% reflection
Rfree0.314 --
Rwork0.286 11208 -
obs--89 %
Refinement
*PLUS
Highest resolution: 2.7 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.007
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.4
X-RAY DIFFRACTIONdihedral_angle_d
X-RAY DIFFRACTIONdihedral_angle_deg24
X-RAY DIFFRACTIONimproper_angle_d
X-RAY DIFFRACTIONimproper_angle_deg1

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