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- PDB-4q3q: Crystal structure of Schistosoma mansoni arginase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4q3q
TitleCrystal structure of Schistosoma mansoni arginase in complex with inhibitor ABH
ComponentsArginase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / arginase-deacetylase fold / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


arginine metabolic process / arginase / arginase activity / urea cycle / metal ion binding
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
2(S)-AMINO-6-BORONOHEXANOIC ACID / : / Arginase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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_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

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Assembly

Deposited unit
A: Arginase
B: Arginase
C: Arginase
D: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,82922
Polymers169,0694
Non-polymers1,76018
Water16,123895
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,26018
Polymers126,8023
Non-polymers1,45815
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 area12310 Å2
ΔGint-64 kcal/mol
Surface area35070 Å2
MethodPISA
2
B: Arginase
hetero molecules

B: Arginase
hetero molecules

B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,26018
Polymers126,8023
Non-polymers1,45815
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 area12220 Å2
ΔGint-64 kcal/mol
Surface area35450 Å2
MethodPISA
3
C: Arginase
hetero molecules

C: Arginase
hetero molecules

C: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,26018
Polymers126,8023
Non-polymers1,45815
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12370 Å2
ΔGint-57 kcal/mol
Surface area35310 Å2
MethodPISA
4
D: Arginase
hetero molecules

D: Arginase
hetero molecules

D: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,70812
Polymers126,8023
Non-polymers9069
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 area10960 Å2
ΔGint-65 kcal/mol
Surface area34300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.224, 178.224, 178.224
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-604-

HOH

21A-609-

HOH

31A-610-

HOH

41B-621-

HOH

51B-624-

HOH

61B-625-

HOH

71B-781-

HOH

81C-544-

HOH

91C-577-

HOH

101C-685-

HOH

111D-517-

HOH

121D-523-

HOH

131D-579-

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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ABH / 2(S)-AMINO-6-BORONOHEXANOIC ACID


Mass: 191.998 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15BNO5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 895 / 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: 55.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% w/v PEG3350, 4% v/v Tacsimate, pH 7.0, 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→50 Å / Num. all: 126488 / Num. obs: 126488 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 23.78 Å2 / Rmerge(I) obs: 0.153 / 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
2-2.079.80.8313.1125430.83199.9
2.07-2.15100.6454125460.645100
2.15-2.2510.30.4715.5125850.471100
2.25-2.3710.60.3747.1125530.374100
2.37-2.5210.80.2879.2126130.287100
2.52-2.71110.23110.9125860.231100
2.71-2.9911.20.17813.5126430.178100
2.99-3.4211.30.1415.4126540.14100
3.42-4.3111.10.10517.4127400.105100
4.31-5011.30.08717.4130250.08799.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4Q3P

4q3p


Resolution: 2.001→49.43 Å / SU ML: 0.22 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.15 / Phase error: 18.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 5927 5 %RANDOM
Rwork0.1684 ---
obs0.17 118487 93.68 %-
all-126455 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.196 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.001→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10241 0 96 895 11232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810507
X-RAY DIFFRACTIONf_angle_d1.21114228
X-RAY DIFFRACTIONf_dihedral_angle_d15.8223898
X-RAY DIFFRACTIONf_chiral_restr0.1111644
X-RAY DIFFRACTIONf_plane_restr0.0051845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.02360.24741840.20833343X-RAY DIFFRACTION84
2.0236-2.04740.25432010.20733436X-RAY DIFFRACTION87
2.0474-2.07240.2291800.19683472X-RAY DIFFRACTION87
2.0724-2.09860.25151800.19343464X-RAY DIFFRACTION87
2.0986-2.12620.24841620.19433508X-RAY DIFFRACTION89
2.1262-2.15540.21781760.18453598X-RAY DIFFRACTION89
2.1554-2.18620.22981860.1813558X-RAY DIFFRACTION90
2.1862-2.21880.21421840.17083615X-RAY DIFFRACTION90
2.2188-2.25350.20032080.17713686X-RAY DIFFRACTION93
2.2535-2.29040.20571910.17343610X-RAY DIFFRACTION90
2.2904-2.32990.2112060.17153568X-RAY DIFFRACTION91
2.3299-2.37230.19841990.17053720X-RAY DIFFRACTION92
2.3723-2.41790.20781990.16783621X-RAY DIFFRACTION92
2.4179-2.46720.2271870.16363726X-RAY DIFFRACTION93
2.4672-2.52090.19682210.1653725X-RAY DIFFRACTION94
2.5209-2.57950.19422160.17253730X-RAY DIFFRACTION94
2.5795-2.6440.19611760.16643809X-RAY DIFFRACTION95
2.644-2.71550.2022120.16613756X-RAY DIFFRACTION95
2.7155-2.79540.21152050.16563852X-RAY DIFFRACTION96
2.7954-2.88560.20142070.173805X-RAY DIFFRACTION96
2.8856-2.98880.2191910.17713862X-RAY DIFFRACTION96
2.9888-3.10840.2062030.17463895X-RAY DIFFRACTION97
3.1084-3.24980.22671930.1683929X-RAY DIFFRACTION98
3.2498-3.42110.17922150.17253946X-RAY DIFFRACTION98
3.4211-3.63540.19212030.15553992X-RAY DIFFRACTION99
3.6354-3.9160.1832050.1463981X-RAY DIFFRACTION99
3.916-4.30990.15651860.14254027X-RAY DIFFRACTION99
4.3099-4.93310.17262080.13244059X-RAY DIFFRACTION100
4.9331-6.21320.17422190.16464070X-RAY DIFFRACTION100
6.2132-49.44550.21582240.1854197X-RAY DIFFRACTION100

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