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- PDB-4q3p: Crystal structure of Schistosoma mansoni arginase -

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Basic information

Entry
Database: PDB / ID: 4q3p
TitleCrystal structure of Schistosoma mansoni arginase
ComponentsArginase
KeywordsHYDROLASE / arginase-deacetylase fold
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
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 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)170,06118
Polymers169,0694
Non-polymers99214
Water8,917495
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,68415
Polymers126,8023
Non-polymers88212
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 area10650 Å2
ΔGint-69 kcal/mol
Surface area35570 Å2
MethodPISA
2
B: Arginase
hetero molecules

B: Arginase
hetero molecules

B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,68415
Polymers126,8023
Non-polymers88212
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 area10730 Å2
ΔGint-67 kcal/mol
Surface area35420 Å2
MethodPISA
3
C: Arginase
hetero molecules

C: Arginase
hetero molecules

C: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,68415
Polymers126,8023
Non-polymers88212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10980 Å2
ΔGint-61 kcal/mol
Surface area35430 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 area9440 Å2
ΔGint-64 kcal/mol
Surface area35890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.384, 178.384, 178.384
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-539-

HOH

21A-679-

HOH

31C-575-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 7.5
Details: 12% w/v PEG20000, 0.1 M imidazole, 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: 2.5→50 Å / Num. all: 65380 / Num. obs: 65315 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 30.45 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.5-2.596.40.8342.16447199.6
2.59-2.696.50.6412.86422199.8
2.69-2.826.60.4923.96504199.8
2.82-2.966.70.3965.26484199.9
2.96-3.156.90.2867.76488199.9
3.15-3.3970.2111.265101100
3.39-3.737.30.16217.365391100
3.73-4.277.80.13225.165501100
4.27-5.388.30.01530.165931100
5.38-508.30.08435.967781100

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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: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PHA

2pha


Resolution: 2.501→49.475 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 3303 5.06 %RANDOM
Rwork0.1771 ---
obs0.179 65276 99.89 %-
all-65285 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.501→49.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10262 0 44 495 10801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310493
X-RAY DIFFRACTIONf_angle_d0.74914215
X-RAY DIFFRACTIONf_dihedral_angle_d12.3683908
X-RAY DIFFRACTIONf_chiral_restr0.0511645
X-RAY DIFFRACTIONf_plane_restr0.0031845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.53630.30431400.24672528X-RAY DIFFRACTION99
2.5363-2.57420.29751420.24272566X-RAY DIFFRACTION100
2.5742-2.61440.28441250.23662544X-RAY DIFFRACTION100
2.6144-2.65720.30061360.21872550X-RAY DIFFRACTION100
2.6572-2.7030.2791240.22312575X-RAY DIFFRACTION100
2.703-2.75220.28211450.22142562X-RAY DIFFRACTION100
2.7522-2.80510.27621520.20662557X-RAY DIFFRACTION100
2.8051-2.86240.24911330.20142556X-RAY DIFFRACTION100
2.8624-2.92460.25541390.20652567X-RAY DIFFRACTION100
2.9246-2.99260.25071240.2022582X-RAY DIFFRACTION100
2.9926-3.06750.26561210.20322565X-RAY DIFFRACTION100
3.0675-3.15040.26921400.1912567X-RAY DIFFRACTION100
3.1504-3.24310.22071380.18082611X-RAY DIFFRACTION100
3.2431-3.34770.21181170.18832560X-RAY DIFFRACTION100
3.3477-3.46740.22081340.1752579X-RAY DIFFRACTION100
3.4674-3.60610.23591360.17032592X-RAY DIFFRACTION100
3.6061-3.77020.19841430.16772583X-RAY DIFFRACTION100
3.7702-3.96890.18431240.1562610X-RAY DIFFRACTION100
3.9689-4.21740.18231310.15062579X-RAY DIFFRACTION100
4.2174-4.54290.18111560.13092586X-RAY DIFFRACTION100
4.5429-4.99960.14351590.13392587X-RAY DIFFRACTION100
4.9996-5.72220.17771560.14882603X-RAY DIFFRACTION100
5.7222-7.20580.19191420.17272643X-RAY DIFFRACTION100
7.2058-49.48450.18741460.18542721X-RAY DIFFRACTION100

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