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- PDB-4q3v: Crystal structure of Schistosoma mansoni arginase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4q3v
TitleCrystal structure of Schistosoma mansoni arginase in complex with inhibitor BEC
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
: / S-2-(BORONOETHYL)-L-CYSTEINE / Arginase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 2.7 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

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)170,69121
Polymers169,0694
Non-polymers1,62217
Water6,359353
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,31418
Polymers126,8023
Non-polymers1,51215
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 area9860 Å2
ΔGint-30 kcal/mol
Surface area35670 Å2
MethodPISA
2
B: Arginase
hetero molecules

B: Arginase
hetero molecules

B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,31418
Polymers126,8023
Non-polymers1,51215
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 area9880 Å2
ΔGint-34 kcal/mol
Surface area36480 Å2
MethodPISA
3
C: Arginase
hetero molecules

C: Arginase
hetero molecules

C: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,31418
Polymers126,8023
Non-polymers1,51215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9990 Å2
ΔGint-27 kcal/mol
Surface area36270 Å2
MethodPISA
4
D: Arginase
hetero molecules

D: Arginase
hetero molecules

D: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,1329
Polymers126,8023
Non-polymers3306
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area9320 Å2
ΔGint-61 kcal/mol
Surface area34920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.392, 178.392, 178.392
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-546-

HOH

21A-599-

HOH

31C-562-

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-S2C / S-2-(BORONOETHYL)-L-CYSTEINE


Type: L-peptide linking / Mass: 210.036 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H13BNO5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 4% v/v Tacsimate, pH 7.0, 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: 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: 2.7→50 Å / Num. all: 52114 / Num. obs: 51489 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 29.97 Å2 / Rmerge(I) obs: 0.158 / Rsym value: 0.158 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.7-2.83.60.65551180.655199.7
2.8-2.913.70.52651710.526199.7
2.91-3.043.70.40351490.403199.5
3.04-3.23.80.3151490.31199.8
3.2-3.43.90.22751390.227199.6
3.4-3.663.90.16151770.161199.4
3.66-4.0340.12651480.126199.2
4.03-4.64.10.10451710.104198.8
4.62-5.814.10.151230.1197.7
5.81-504.20.0851440.08194.8

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Processing

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

4q3p


Resolution: 2.7→49.477 Å / SU ML: 0.32 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 2636 5.12 %RANDOM
Rwork0.1672 ---
obs0.1698 51451 98.79 %-
all-51457 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10303 0 83 353 10739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310564
X-RAY DIFFRACTIONf_angle_d0.88314305
X-RAY DIFFRACTIONf_dihedral_angle_d13.293943
X-RAY DIFFRACTIONf_chiral_restr0.0861653
X-RAY DIFFRACTIONf_plane_restr0.0031853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74890.31241570.24112571X-RAY DIFFRACTION100
2.7489-2.80180.27891410.22622539X-RAY DIFFRACTION100
2.8018-2.8590.28851330.22222577X-RAY DIFFRACTION100
2.859-2.92110.28281470.23582565X-RAY DIFFRACTION100
2.9211-2.98910.26591500.2042554X-RAY DIFFRACTION100
2.9891-3.06380.2441450.20332554X-RAY DIFFRACTION100
3.0638-3.14660.24891500.18992558X-RAY DIFFRACTION100
3.1466-3.23920.24541500.17992583X-RAY DIFFRACTION100
3.2392-3.34370.24221200.18882566X-RAY DIFFRACTION100
3.3437-3.46320.25211360.18042596X-RAY DIFFRACTION100
3.4632-3.60180.24861320.17872569X-RAY DIFFRACTION99
3.6018-3.76570.22591410.16522607X-RAY DIFFRACTION99
3.7657-3.96410.21591100.14752576X-RAY DIFFRACTION99
3.9641-4.21240.19551460.13872574X-RAY DIFFRACTION100
4.2124-4.53740.14781610.122561X-RAY DIFFRACTION99
4.5374-4.99370.16641380.11892560X-RAY DIFFRACTION98
4.9937-5.71530.16181220.13982568X-RAY DIFFRACTION97
5.7153-7.19720.19991320.16572555X-RAY DIFFRACTION96
7.1972-49.48530.18291250.15842582X-RAY DIFFRACTION93

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