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- PDB-5zee: Crystal structure of Entamoeba histolytica Arginase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5zee
TitleCrystal structure of Entamoeba histolytica Arginase in complex with N(omega)-hydroxy-L-arginine (NOHA) at 1.74 A
ComponentsArginase
KeywordsHYDROLASE/INHIBITOR / Metalloenzyme / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / manganese ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ureohydrolase domain / Arginase / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-OMEGA-HYDROXY-L-ARGININE / : / Arginase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsMalik, A. / Dalal, V. / Ankri, S. / Tomar, S.
CitationJournal: Febs J. / Year: 2019
Title: Structural insights into Entamoeba histolytica arginase and structure-based identification of novel non-amino acid based inhibitors as potential antiamoebic molecules.
Authors: Malik, A. / Dalal, V. / Ankri, S. / Tomar, S.
History
DepositionFeb 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,50212
Polymers69,6542
Non-polymers84810
Water6,359353
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint7 kcal/mol
Surface area22810 Å2
Unit cell
Length a, b, c (Å)87.722, 97.538, 125.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 1 - 294 / Label seq-ID: 17 - 310

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Arginase


Mass: 34826.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_152330 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: C4LSS0, arginase
#2: Chemical ChemComp-HAR / N-OMEGA-HYDROXY-L-ARGININE


Type: L-peptide linking / Mass: 190.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14N4O3
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#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: 2.04 Å3/Da / Density % sol: 35.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M bistris propane (pH- 6.5), 0.2M potassium thiocyanate, 22% Peg 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.74→45.14 Å / Num. obs: 55347 / % possible obs: 99.4 % / Redundancy: 5.72 % / Biso Wilson estimate: 39.3 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.58
Reflection shellResolution: 1.74→1.84 Å / Mean I/σ(I) obs: 2.1 / CC1/2: 0.98 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CEV

1cev


Resolution: 1.74→45.14 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 7.663 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19266 2098 3.8 %RANDOM
Rwork0.15571 ---
obs0.15715 53212 99.34 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 39.828 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0 Å20 Å2
2---2.28 Å2-0 Å2
3---2.74 Å2
Refinement stepCycle: 1 / Resolution: 1.74→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4606 0 46 353 5005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194893
X-RAY DIFFRACTIONr_bond_other_d0.0020.024727
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.9876603
X-RAY DIFFRACTIONr_angle_other_deg0.994311054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22626.04202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75715899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.51512
X-RAY DIFFRACTIONr_chiral_restr0.1090.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215341
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02849
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4162.2692426
X-RAY DIFFRACTIONr_mcbond_other2.4162.2692426
X-RAY DIFFRACTIONr_mcangle_it3.0893.383042
X-RAY DIFFRACTIONr_mcangle_other3.0893.383043
X-RAY DIFFRACTIONr_scbond_it4.4782.8172467
X-RAY DIFFRACTIONr_scbond_other4.4742.8172467
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1273.9663550
X-RAY DIFFRACTIONr_long_range_B_refined8.0429.0315462
X-RAY DIFFRACTIONr_long_range_B_other7.97528.6545418
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19846 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.736→1.781 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 146 -
Rwork0.461 3716 -
obs--94.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.75630.2962-0.06531.96120.45961.33420.148-0.13970.03740.239-0.163-0.0965-0.03730.06220.0150.0979-0.0642-0.02420.10860.02090.0114-0.6715.059-6.619
21.9507-0.3595-0.58121.96580.4051.1482-0.1355-0.1077-0.014-0.02690.13260.02840.00050.12980.00290.01410.001-0.00320.17840.06110.027824.479-22.72-23.134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 295
2X-RAY DIFFRACTION2B-1 - 295

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