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- PDB-4q40: Crystal structure of Schistosoma mansoni arginase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4q40
TitleCrystal structure of Schistosoma mansoni arginase in complex with L-valine
ComponentsArginase
KeywordsHYDROLASE / arginase-deacetylase fold
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
IMIDAZOLE / : / VALINE / Arginase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.831 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)171,10630
Polymers169,0694
Non-polymers2,03626
Water18,3571019
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,72627
Polymers126,8023
Non-polymers1,92424
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12050 Å2
ΔGint-48 kcal/mol
Surface area35500 Å2
MethodPISA
2
B: Arginase
hetero molecules

B: Arginase
hetero molecules

B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,65727
Polymers126,8023
Non-polymers1,85524
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12590 Å2
ΔGint-40 kcal/mol
Surface area35080 Å2
MethodPISA
3
C: Arginase
hetero molecules

C: Arginase
hetero molecules

C: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,45024
Polymers126,8023
Non-polymers1,64821
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 area12110 Å2
ΔGint-53 kcal/mol
Surface area35270 Å2
MethodPISA
4
D: Arginase
hetero molecules

D: Arginase
hetero molecules

D: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,48312
Polymers126,8023
Non-polymers6819
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 area9290 Å2
ΔGint-59 kcal/mol
Surface area34980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.808, 177.808, 177.808
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-672-

HOH

21A-675-

HOH

31A-802-

HOH

41B-704-

HOH

51B-746-

HOH

61B-795-

HOH

71C-624-

HOH

81C-641-

HOH

91D-559-

HOH

101D-595-

HOH

111D-613-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 1045 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-VAL / VALINE / Valine


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H11NO2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1019 / 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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: crystal soaked in 50 mM L-valine, 14% 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: Oct 24, 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: 1.83→50 Å / Num. all: 163655 / Num. obs: 163491 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 21.41 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.83-1.950.8132.1161800.81399.9
1.9-1.9750.5593162220.55999.9
1.97-2.0650.3674.5162510.36799.9
2.06-2.1750.276162850.27100
2.17-2.3150.1878.4162890.18799.9
2.31-2.4850.14310.9163260.143100
2.48-2.7350.11213.1163400.11299.9
2.73-3.1350.0915.7163560.0999.9
3.13-3.9450.07416.6164670.07499.9
3.94-504.90.05222.1167750.05299.8

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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: 1.831→49.315 Å / SU ML: 0.18 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 18.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 7678 5.03 %RANDOM
Rwork0.174 ---
obs0.1751 152572 93.27 %-
all-163446 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.473 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.831→49.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10252 0 117 1019 11388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710550
X-RAY DIFFRACTIONf_angle_d1.02614273
X-RAY DIFFRACTIONf_dihedral_angle_d15.123901
X-RAY DIFFRACTIONf_chiral_restr0.0711647
X-RAY DIFFRACTIONf_plane_restr0.0051856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.831-1.85150.26522050.25464098X-RAY DIFFRACTION80
1.8515-1.87330.29142110.23914258X-RAY DIFFRACTION82
1.8733-1.89620.24542220.22064233X-RAY DIFFRACTION83
1.8962-1.92020.25592140.21524416X-RAY DIFFRACTION85
1.9202-1.94540.24392300.20764470X-RAY DIFFRACTION86
1.9454-1.97210.23252530.20174360X-RAY DIFFRACTION86
1.9721-2.00030.2362460.19624636X-RAY DIFFRACTION90
2.0003-2.03010.24912340.18754657X-RAY DIFFRACTION91
2.0301-2.06180.20852640.18184681X-RAY DIFFRACTION91
2.0618-2.09570.20682510.17814722X-RAY DIFFRACTION91
2.0957-2.13180.21642480.1734739X-RAY DIFFRACTION92
2.1318-2.17060.21162410.17184804X-RAY DIFFRACTION93
2.1706-2.21230.21312630.16674817X-RAY DIFFRACTION94
2.2123-2.25750.19192580.16334884X-RAY DIFFRACTION95
2.2575-2.30650.19032600.16334871X-RAY DIFFRACTION95
2.3065-2.36020.17942800.16614864X-RAY DIFFRACTION95
2.3602-2.41920.21962720.16334973X-RAY DIFFRACTION96
2.4192-2.48460.19052800.16534912X-RAY DIFFRACTION96
2.4846-2.55770.19562530.1664967X-RAY DIFFRACTION96
2.5577-2.64030.20432280.17055028X-RAY DIFFRACTION96
2.6403-2.73470.20042400.17725042X-RAY DIFFRACTION97
2.7347-2.84410.19872730.17165031X-RAY DIFFRACTION98
2.8441-2.97360.2062680.17915066X-RAY DIFFRACTION98
2.9736-3.13030.18572670.17665086X-RAY DIFFRACTION98
3.1303-3.32640.19752960.17225120X-RAY DIFFRACTION99
3.3264-3.58320.16542780.16855152X-RAY DIFFRACTION99
3.5832-3.94360.17442830.15115193X-RAY DIFFRACTION99
3.9436-4.51390.14532590.14795196X-RAY DIFFRACTION99
4.5139-5.68570.17323070.16055235X-RAY DIFFRACTION100
5.6857-49.33290.192940.18555383X-RAY DIFFRACTION99

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