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- PDB-4q3u: Crystal structure of Schistosoma mansoni arginase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4q3u
TitleCrystal structure of Schistosoma mansoni arginase in complex with inhibitor nor-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
: / NOR-N-OMEGA-HYDROXY-L-ARGININE / Arginase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)170,76622
Polymers169,0694
Non-polymers1,69718
Water7,026390
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,21318
Polymers126,8023
Non-polymers1,41115
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 area9950 Å2
ΔGint-26 kcal/mol
Surface area35370 Å2
MethodPISA
2
B: Arginase
hetero molecules

B: Arginase
hetero molecules

B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,21318
Polymers126,8023
Non-polymers1,41115
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 area9980 Å2
ΔGint-39 kcal/mol
Surface area35820 Å2
MethodPISA
3
C: Arginase
hetero molecules

C: Arginase
hetero molecules

C: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,21318
Polymers126,8023
Non-polymers1,41115
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 area9970 Å2
ΔGint-33 kcal/mol
Surface area35590 Å2
MethodPISA
4
D: Arginase
hetero molecules

D: Arginase
hetero molecules

D: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,66012
Polymers126,8023
Non-polymers8589
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 area6580 Å2
ΔGint-17 kcal/mol
Surface area34090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.318, 178.318, 178.318
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-510-

HOH

21A-640-

HOH

31B-597-

HOH

41C-546-

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-NNH / NOR-N-OMEGA-HYDROXY-L-ARGININE


Type: L-peptide linking / Mass: 176.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12N4O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 55.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M L-proline, 0.1 M HEPES, pH 7.5, 10% 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: 2.5→50 Å / Num. all: 65396 / Num. obs: 61734 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 36.36 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.5-2.593.60.715256320.71587
2.59-2.694.20.62.857700.688.8
2.69-2.824.60.446458760.44691.2
2.82-2.9650.3495.460230.34992.7
2.96-3.155.30.2617.861390.26194.3
3.15-3.395.40.19710.561570.19794.8
3.39-3.735.50.14911.962630.14995.8
3.73-4.276.30.1215.865190.1299.5
4.27-5.389.80.09523.765780.095100
5.38-5011.60.07529.967770.075100

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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: 2.5→49.457 Å / SU ML: 0.31 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 3100 5.06 %RANDOM
Rwork0.1741 ---
obs0.1767 61299 93.82 %-
all-61418 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10147 0 92 390 10629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810451
X-RAY DIFFRACTIONf_angle_d1.09314155
X-RAY DIFFRACTIONf_dihedral_angle_d13.7043894
X-RAY DIFFRACTIONf_chiral_restr0.0411634
X-RAY DIFFRACTIONf_plane_restr0.0051839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5390.29051350.21722410X-RAY DIFFRACTION86
2.539-2.58060.29151310.22162415X-RAY DIFFRACTION87
2.5806-2.62510.26651190.22342497X-RAY DIFFRACTION88
2.6251-2.67280.30541320.22132475X-RAY DIFFRACTION89
2.6728-2.72420.33421280.23012528X-RAY DIFFRACTION90
2.7242-2.77980.31371420.22632531X-RAY DIFFRACTION91
2.7798-2.84020.29021420.21112542X-RAY DIFFRACTION91
2.8402-2.90630.30351370.22562582X-RAY DIFFRACTION92
2.9063-2.9790.28521330.22942610X-RAY DIFFRACTION93
2.979-3.05950.29241210.22442631X-RAY DIFFRACTION93
3.0595-3.14950.32981390.21752640X-RAY DIFFRACTION94
3.1495-3.25120.29861390.21912619X-RAY DIFFRACTION93
3.2512-3.36730.27761260.22392630X-RAY DIFFRACTION93
3.3673-3.50210.28481410.20172650X-RAY DIFFRACTION94
3.5021-3.66150.26051350.18812639X-RAY DIFFRACTION94
3.6615-3.85440.19851550.16682746X-RAY DIFFRACTION97
3.8544-4.09580.19521240.15462784X-RAY DIFFRACTION99
4.0958-4.41190.1761610.13052818X-RAY DIFFRACTION99
4.4119-4.85550.16721800.11892797X-RAY DIFFRACTION99
4.8555-5.55730.17421580.13052812X-RAY DIFFRACTION100
5.5573-6.99850.17671600.14452882X-RAY DIFFRACTION100
6.9985-49.46620.16561620.1442961X-RAY DIFFRACTION100

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