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- PDB-4q3t: Crystal structure of Schistosoma mansoni arginase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4q3t
TitleCrystal structure of Schistosoma mansoni arginase in complex with inhibitor NOHA
ComponentsArginase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / arginase-deacetylase fold / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / manganese ion binding / nucleus / cytosol
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
N-OMEGA-HYDROXY-L-ARGININE / : / Arginase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 2.142 Å
AuthorsHai, Y. / Edwards, J.E. / Van Zandt, M.C. / Hoffmann, K.F. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2014
Title: Crystal Structure of Schistosoma mansoni Arginase, a Potential Drug Target for the Treatment of Schistosomiasis.
Authors: Hai, Y. / Edwards, J.E. / Van Zandt, M.C. / Hoffmann, K.F. / Christianson, D.W.
History
DepositionApr 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif / 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_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _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
B: Arginase
C: Arginase
D: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,82222
Polymers169,0694
Non-polymers1,75318
Water10,935607
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,25518
Polymers126,8023
Non-polymers1,45315
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area9960 Å2
ΔGint-35 kcal/mol
Surface area35410 Å2
MethodPISA
2
B: Arginase
hetero molecules

B: Arginase
hetero molecules

B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,25518
Polymers126,8023
Non-polymers1,45315
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area10030 Å2
ΔGint-32 kcal/mol
Surface area35560 Å2
MethodPISA
3
C: Arginase
hetero molecules

C: Arginase
hetero molecules

C: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,25518
Polymers126,8023
Non-polymers1,45315
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10010 Å2
ΔGint-33 kcal/mol
Surface area35650 Å2
MethodPISA
4
D: Arginase
hetero molecules

D: Arginase
hetero molecules

D: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,70212
Polymers126,8023
Non-polymers9009
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area8360 Å2
ΔGint-24 kcal/mol
Surface area34580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.762, 177.762, 177.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

21B-673-

HOH

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Components

#1: Protein
Arginase


Mass: 42267.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_059980 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WVP6, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-HAR / N-OMEGA-HYDROXY-L-ARGININE


Type: L-peptide linking / Mass: 190.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14N4O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M Bis-Tris, pH 6.5, 10% w/v PEG10000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2012 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. all: 102500 / Num. obs: 102397 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 23.46 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.15 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.14-2.225.20.8832101230.88399.6
2.22-2.315.30.6982.6101590.69899.7
2.31-2.415.40.5553.3100980.55599.8
2.41-2.545.50.4234.5102400.42399.9
2.54-2.715.60.3275.8101570.327100
2.7-2.95.80.2368.2102100.236100
2.9-3.260.16512102290.165100
3.2-3.666.20.11218.1102790.112100
3.66-4.616.70.09222.5103210.092100
4.61-506.80.06726.6105810.067100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: PHASER
Starting model: PDB ENTRY 4Q3P

4q3p


Resolution: 2.142→49.302 Å / SU ML: 0.22 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.209 5117 5 %RANDOM
Rwork0.1761 ---
obs0.1778 102353 99.89 %-
all-102362 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2.142→49.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10230 0 96 607 10933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410551
X-RAY DIFFRACTIONf_angle_d0.88614281
X-RAY DIFFRACTIONf_dihedral_angle_d13.0063919
X-RAY DIFFRACTIONf_chiral_restr0.0571646
X-RAY DIFFRACTIONf_plane_restr0.0031857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.142-2.16650.29251680.24813252X-RAY DIFFRACTION100
2.1665-2.1920.28771690.24053196X-RAY DIFFRACTION100
2.192-2.21870.29521960.22833183X-RAY DIFFRACTION100
2.2187-2.24680.261790.22773204X-RAY DIFFRACTION100
2.2468-2.27640.26441390.21233250X-RAY DIFFRACTION100
2.2764-2.30760.24561700.2123175X-RAY DIFFRACTION100
2.3076-2.34050.26361960.21533228X-RAY DIFFRACTION100
2.3405-2.37550.22971770.20183187X-RAY DIFFRACTION100
2.3755-2.41260.25811550.20223229X-RAY DIFFRACTION100
2.4126-2.45210.25521660.19923193X-RAY DIFFRACTION100
2.4521-2.49440.24191650.18923221X-RAY DIFFRACTION100
2.4944-2.53980.24611780.19483256X-RAY DIFFRACTION100
2.5398-2.58860.25681650.19873206X-RAY DIFFRACTION100
2.5886-2.64150.24391660.19223246X-RAY DIFFRACTION100
2.6415-2.69890.21871800.18493193X-RAY DIFFRACTION100
2.6989-2.76170.22491890.17713227X-RAY DIFFRACTION100
2.7617-2.83070.2021750.16663232X-RAY DIFFRACTION100
2.8307-2.90730.23641630.18513217X-RAY DIFFRACTION100
2.9073-2.99280.2341730.18353270X-RAY DIFFRACTION100
2.9928-3.08940.22131350.1813237X-RAY DIFFRACTION100
3.0894-3.19980.21331430.18193257X-RAY DIFFRACTION100
3.1998-3.32790.21921710.18143251X-RAY DIFFRACTION100
3.3279-3.47930.21591680.16973249X-RAY DIFFRACTION100
3.4793-3.66270.20241810.16333255X-RAY DIFFRACTION100
3.6627-3.89210.17211740.15033255X-RAY DIFFRACTION100
3.8921-4.19240.16061740.14273279X-RAY DIFFRACTION100
4.1924-4.6140.13761690.12993265X-RAY DIFFRACTION100
4.614-5.2810.15851930.14423267X-RAY DIFFRACTION100
5.281-6.6510.18531590.1743335X-RAY DIFFRACTION100
6.651-49.31530.19431810.17753421X-RAY DIFFRACTION100

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