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- PDB-4q3s: Crystal structure of Schistosoma mansoni arginase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4q3s
TitleCrystal structure of Schistosoma mansoni arginase in complex with inhibitor ABHPE
ComponentsArginase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / arginase-deacetylase fold / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


arginase / arginase activity / : / urea cycle / manganese ion binding / nucleus / 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
: / Chem-X7A / Arginase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 1.3May 1, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.4Sep 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_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_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_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)171,45824
Polymers169,0694
Non-polymers2,38920
Water15,295849
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,87021
Polymers126,8023
Non-polymers2,06818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area10640 Å2
ΔGint-41 kcal/mol
Surface area35180 Å2
MethodPISA
2
B: Arginase
hetero molecules

B: Arginase
hetero molecules

B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,87021
Polymers126,8023
Non-polymers2,06818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area10730 Å2
ΔGint-38 kcal/mol
Surface area35610 Å2
MethodPISA
3
C: Arginase
hetero molecules

C: Arginase
hetero molecules

C: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,59418
Polymers126,8023
Non-polymers1,79215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area10210 Å2
ΔGint-31 kcal/mol
Surface area35180 Å2
MethodPISA
4
D: Arginase
hetero molecules

D: Arginase
hetero molecules

D: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,04112
Polymers126,8023
Non-polymers1,2399
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_456z-1,x,y+11
crystal symmetry operation9_546y,z-1,x+11
Buried area8750 Å2
ΔGint-27 kcal/mol
Surface area34690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.212, 178.212, 178.212
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-534-

HOH

21A-550-

HOH

31B-528-

HOH

41B-530-

HOH

51C-505-

HOH

61C-541-

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-X7A / [(5R)-5-amino-5-carboxy-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-)


Mass: 303.183 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H28BN2O5
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 849 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M HEPES, pH 7.4, 12% w/v PEG3350, 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: Mar 24, 2014 / 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: 2.11→50 Å / Num. all: 108015 / Num. obs: 106395 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 24.59 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.11-2.275.30.7572102430.75796.1
2.19-2.275.60.5573103560.55796.1
2.27-2.385.70.4583.7103860.45896.8
2.38-2.560.3465.1104660.34698
2.5-2.666.30.2746.6106380.27498.7
2.66-2.8670.2079.4107150.20799.5
2.86-3.158.40.16413.1107430.16499.9
3.15-3.6110.60.11519.6108500.115100
3.61-4.5415.50.08628.6108780.086100
4.54-50220.07535.1111200.075100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4Q3P

4q3p


Resolution: 2.11→49.427 Å / SU ML: 0.19 / Isotropic thermal model: ISOTROPIC / Cross valid method: THOUGHOUT / σ(F): 1.34 / Phase error: 21.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 5301 4.99 %RANDOM
Rwork0.1732 ---
obs0.1749 106337 98.5 %-
all-106351 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.9 Å2
Refinement stepCycle: LAST / Resolution: 2.11→49.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10222 0 140 849 11211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410590
X-RAY DIFFRACTIONf_angle_d0.83914350
X-RAY DIFFRACTIONf_dihedral_angle_d15.4443996
X-RAY DIFFRACTIONf_chiral_restr0.0331645
X-RAY DIFFRACTIONf_plane_restr0.0031855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.13410.25841820.23223256X-RAY DIFFRACTION96
2.1341-2.15920.30261770.22493248X-RAY DIFFRACTION96
2.1592-2.18550.29051400.21853288X-RAY DIFFRACTION96
2.1855-2.21320.24541490.21213289X-RAY DIFFRACTION96
2.2132-2.24230.25931800.20413241X-RAY DIFFRACTION96
2.2423-2.2730.24731920.1953253X-RAY DIFFRACTION96
2.273-2.30550.2211800.19623270X-RAY DIFFRACTION97
2.3055-2.33990.23531790.20263294X-RAY DIFFRACTION97
2.3399-2.37650.23931500.19433333X-RAY DIFFRACTION97
2.3765-2.41540.23971740.19423318X-RAY DIFFRACTION98
2.4154-2.45710.23231910.19113302X-RAY DIFFRACTION98
2.4571-2.50170.22171540.18153330X-RAY DIFFRACTION99
2.5017-2.54990.22471870.19233370X-RAY DIFFRACTION98
2.5499-2.60190.25691590.19433351X-RAY DIFFRACTION99
2.6019-2.65850.21781880.18353385X-RAY DIFFRACTION99
2.6585-2.72030.2281820.19163337X-RAY DIFFRACTION99
2.7203-2.78830.22771790.19043436X-RAY DIFFRACTION100
2.7883-2.86370.28381710.18553385X-RAY DIFFRACTION99
2.8637-2.9480.23551700.19563362X-RAY DIFFRACTION100
2.948-3.04310.22051790.18613421X-RAY DIFFRACTION100
3.0431-3.15190.25071840.1873437X-RAY DIFFRACTION100
3.1519-3.2780.20511850.17913406X-RAY DIFFRACTION100
3.278-3.42720.20161620.17763452X-RAY DIFFRACTION100
3.4272-3.60780.18511680.16453448X-RAY DIFFRACTION100
3.6078-3.83380.19421990.15813420X-RAY DIFFRACTION100
3.8338-4.12970.15551800.14873405X-RAY DIFFRACTION100
4.1297-4.5450.13791850.12933473X-RAY DIFFRACTION100
4.545-5.2020.17822070.13653419X-RAY DIFFRACTION100
5.202-6.55160.20591660.16263522X-RAY DIFFRACTION100
6.5516-49.44070.16552020.15973585X-RAY DIFFRACTION100

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