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- PDB-4q42: Crystal structure of Schistosoma mansoni arginase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4q42
TitleCrystal structure of Schistosoma mansoni arginase in complex with L-ornithine
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
: / L-ornithine / Arginase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 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)170,59022
Polymers169,0694
Non-polymers1,52118
Water12,232679
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,08118
Polymers126,8023
Non-polymers1,27915
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 area10360 Å2
ΔGint-58 kcal/mol
Surface area35740 Å2
MethodPISA
2
B: Arginase
hetero molecules

B: Arginase
hetero molecules

B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,08118
Polymers126,8023
Non-polymers1,27915
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 area10440 Å2
ΔGint-54 kcal/mol
Surface area35540 Å2
MethodPISA
3
C: Arginase
hetero molecules

C: Arginase
hetero molecules

C: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,08118
Polymers126,8023
Non-polymers1,27915
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 area10490 Å2
ΔGint-56 kcal/mol
Surface area35790 Å2
MethodPISA
4
D: Arginase
hetero molecules

D: Arginase
hetero molecules

D: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,52812
Polymers126,8023
Non-polymers7269
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 area9230 Å2
ΔGint-65 kcal/mol
Surface area35110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.447, 178.447, 178.447
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-615-

HOH

21A-620-

HOH

31A-682-

HOH

41B-520-

HOH

51B-613-

HOH

61B-727-

HOH

71C-606-

HOH

81C-642-

HOH

91D-544-

HOH

101D-561-

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-ORN / L-ornithine / Ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12N2O2
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 679 / 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: 56.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: crystal soaked in 50 mM L-ornithine, 0.1 M imidazole, pH 7.0, 14% w/v PEG20000 for one day, 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: 2.05→50 Å / Num. all: 118020 / Num. obs: 118020 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 26.85 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.05-2.1212.40.793.8117081100
2.12-2.2112.40.5845.2116981100
2.21-2.3112.40.4257.2116931100
2.31-2.4312.40.3418.7117511100
2.43-2.5812.40.2611.6117311100
2.58-2.7812.40.20213.9117941100
2.78-3.0612.40.14618.6117751100
3.06-3.5112.40.11221.8118321100
3.51-4.4212.30.09324.3118901100
4.42-5012.10.06331.3121481100

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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: 2.051→49.492 Å / SU ML: 0.25 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.21 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 5586 5 %RANDOM
Rwork0.1739 ---
obs0.1756 111704 94.68 %-
all-117973 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.339 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.051→49.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10259 0 80 679 11018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610545
X-RAY DIFFRACTIONf_angle_d0.93414279
X-RAY DIFFRACTIONf_dihedral_angle_d15.453927
X-RAY DIFFRACTIONf_chiral_restr0.0641648
X-RAY DIFFRACTIONf_plane_restr0.0041856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.051-2.07390.23531640.20363217X-RAY DIFFRACTION87
2.0739-2.09830.23731650.19663227X-RAY DIFFRACTION87
2.0983-2.12390.25521640.18843262X-RAY DIFFRACTION88
2.1239-2.15070.22141780.18163300X-RAY DIFFRACTION89
2.1507-2.1790.21911850.18473301X-RAY DIFFRACTION90
2.179-2.20890.2651750.17853337X-RAY DIFFRACTION90
2.2089-2.24050.24651810.17193414X-RAY DIFFRACTION91
2.2405-2.27390.19151680.15913424X-RAY DIFFRACTION93
2.2739-2.30940.22281630.16443428X-RAY DIFFRACTION92
2.3094-2.34730.19971910.16793442X-RAY DIFFRACTION92
2.3473-2.38780.21152080.16693412X-RAY DIFFRACTION93
2.3878-2.43120.20471770.16743451X-RAY DIFFRACTION93
2.4312-2.47790.21421950.16583520X-RAY DIFFRACTION95
2.4779-2.52850.18941840.16763535X-RAY DIFFRACTION95
2.5285-2.58350.22612070.16713456X-RAY DIFFRACTION94
2.5835-2.64360.211820.17433532X-RAY DIFFRACTION95
2.6436-2.70970.23941670.17873625X-RAY DIFFRACTION96
2.7097-2.7830.21141830.17923578X-RAY DIFFRACTION96
2.783-2.86480.23691870.17313634X-RAY DIFFRACTION97
2.8648-2.95730.22451750.18363608X-RAY DIFFRACTION97
2.9573-3.0630.21611920.18423644X-RAY DIFFRACTION97
3.063-3.18560.24632040.18763676X-RAY DIFFRACTION98
3.1856-3.33050.23532000.18583654X-RAY DIFFRACTION99
3.3305-3.50610.21071930.17793722X-RAY DIFFRACTION99
3.5061-3.72570.20191880.16613705X-RAY DIFFRACTION99
3.7257-4.01320.19771820.1523760X-RAY DIFFRACTION100
4.0132-4.41690.17192030.14413768X-RAY DIFFRACTION99
4.4169-5.05550.15571990.1443776X-RAY DIFFRACTION100
5.0555-6.36720.18132060.17023799X-RAY DIFFRACTION100
6.3672-49.50670.19472200.23911X-RAY DIFFRACTION100

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