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

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Basic information

Entry
Database: PDB / ID: 5zef
TitleCrystal structure of Entamoeba histolytica Arginase in complex with L- Norvaline at 2.01 A
ComponentsArginase
KeywordsHYDROLASE / Entamoeba histolytica / Metalloenzyme / Inhibition
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
: / NORVALINE / Arginase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginase
B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,41612
Polymers69,6542
Non-polymers76210
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-20 kcal/mol
Surface area22120 Å2
Unit cell
Length a, b, c (Å)87.947, 98.358, 135.329
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A0 - 294
2010B0 - 294

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Arginase


Mass: 34826.906 Da / Num. of mol.: 2 / Fragment: UNP residues 1-295
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

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Non-polymers , 5 types, 302 molecules

#2: Chemical ChemComp-NVA / NORVALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1M bistris propane pH-6.2, 0.2M potassium thiocyanate, 20% 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: 2.01→41 Å / Num. obs: 39225 / % possible obs: 99.6 % / Redundancy: 5.3 % / CC1/2: 0.99 / Net I/σ(I): 12.8
Reflection shellResolution: 2.01→2.04 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1876 / CC1/2: 0.97 / % possible all: 97.5

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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: 2.01→41 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 13.955 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.158 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21034 1840 4.7 %RANDOM
Rwork0.17855 ---
obs0.18012 37164 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.554 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å20 Å2
2---1.66 Å2-0 Å2
3---2.55 Å2
Refinement stepCycle: 1 / Resolution: 2.01→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4597 0 40 292 4929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194781
X-RAY DIFFRACTIONr_bond_other_d0.0020.024590
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9826442
X-RAY DIFFRACTIONr_angle_other_deg1.075310721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2325599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56225.98199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6115872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8511512
X-RAY DIFFRACTIONr_chiral_restr0.1280.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02832
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_it1.9382.2652396
X-RAY DIFFRACTIONr_mcbond_other1.9342.2652396
X-RAY DIFFRACTIONr_mcangle_it2.8133.3772995
X-RAY DIFFRACTIONr_mcangle_other2.8133.3782996
X-RAY DIFFRACTIONr_scbond_it3.0922.612385
X-RAY DIFFRACTIONr_scbond_other3.0872.612385
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3723.7343448
X-RAY DIFFRACTIONr_long_range_B_refined6.82727.9715272
X-RAY DIFFRACTIONr_long_range_B_other6.82327.975272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19728 / 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: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 108 -
Rwork0.345 2665 -
obs--97.09 %
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)
14.31012.2621-1.05849.9587-1.59422.11040.02560.0289-0.0482-0.37720.022-0.3416-0.03790.087-0.04760.0669-0.02190.01350.0453-0.06950.25576.639-1.36716.759
21.81230.0436-0.08943.51610.35311.0546-0.03680.0017-0.0298-0.45310.04160.35170.0483-0.1005-0.00470.1386-0.0423-0.06040.02250.02840.3916-5.802-5.16413.118
32.2802-0.2078-0.19683.8153-0.17251.3580.0080.3654-0.0089-1.23440.0918-0.12170.057-0.0401-0.09980.5218-0.0840.02380.0793-0.00540.34972.623-7.2570.324
43.7824-4.14231.712810.247-5.68976.6281-0.11810.10350.2771-0.3456-0.1149-0.702-0.26560.32080.2330.3559-0.10890.09090.2352-0.00940.395713.957-1.5844.659
59.59641.6297-3.32385.8052-0.78731.9838-0.14690.0056-0.2219-0.40640.0763-0.4030.02330.03150.07060.0861-0.013-0.02190.0442-0.03120.336221.19215.40217.389
64.15720.3488-1.57955.50791.3971.0944-0.235-0.1942-0.1538-0.27620.17650.16680.11110.05170.05840.1854-0.0935-0.01040.1230.00290.489612.15610.70321.679
715.20596.05510.297412.78986.46557.0003-0.2651.8543-0.8217-1.30630.7049-1.9455-0.4380.8537-0.43990.61790.00710.29510.51150.04230.734131.47225.8285.492
82.27550.05330.80114.2128-0.26180.9023-0.1105-0.00580.3315-0.32010.0703-0.35-0.086-0.07180.04020.0429-0.00220.04160.0126-0.02990.556220.64628.74321.354
92.7129-0.21520.7064.8162-0.25081.7165-0.0065-0.25170.37990.32310.0345-0.82220.00930.0479-0.0280.0380.0052-0.05840.0349-0.09080.815229.84531.46730.959
102.8687-0.6515-0.68144.597-0.03291.7603-0.0462-0.2791-0.20480.27770.0493-0.45790.1764-0.0814-0.00310.0454-0.0133-0.0360.0451-0.01890.63425.85415.83330.009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 31
2X-RAY DIFFRACTION2A32 - 190
3X-RAY DIFFRACTION3A191 - 277
4X-RAY DIFFRACTION4A278 - 294
5X-RAY DIFFRACTION5B0 - 31
6X-RAY DIFFRACTION6B32 - 50
7X-RAY DIFFRACTION7B51 - 66
8X-RAY DIFFRACTION8B67 - 139
9X-RAY DIFFRACTION9B140 - 213
10X-RAY DIFFRACTION10B214 - 295

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