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- PDB-8ctm: Crystal structure of the nucleoside hydrolase from Leishmania don... -

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Basic information

Entry
Database: PDB / ID: 8ctm
TitleCrystal structure of the nucleoside hydrolase from Leishmania donovani.
ComponentsInosine-uridine preferring nucleoside hydrolase
KeywordsHYDROLASE / ALPHA/BETA FOLD / LEISHMANIA
Function / homology
Function and homology information


purine nucleosidase / uridine nucleosidase activity / purine nucleosidase activity / nucleobase-containing compound metabolic process / metal ion binding
Similarity search - Function
Inosine/uridine-preferring nucleoside hydrolase, conserved site / Inosine-uridine preferring nucleoside hydrolase family signature. / Inosine-uridine Nucleoside N-ribohydrolase; Chain A / Ribonucleoside hydrolase-like / Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Inosine-uridine preferring nucleoside hydrolase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsChen, Y. / Tolbert, W.D. / Pazgier, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the nucleoside hydrolase from Leishmania donovani.
Authors: Chen, Y. / Tolbert, W.D. / Pazgier, M.
History
DepositionMay 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine-uridine preferring nucleoside hydrolase
B: Inosine-uridine preferring nucleoside hydrolase
C: Inosine-uridine preferring nucleoside hydrolase
D: Inosine-uridine preferring nucleoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,55220
Polymers137,1144
Non-polymers1,43816
Water15,151841
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-112 kcal/mol
Surface area45570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.221, 79.111, 107.621
Angle α, β, γ (deg.)90.00, 90.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Inosine-uridine preferring nucleoside hydrolase / Inosine-uridine preferring nucleoside hydrolase family protein / Nonspecific nucleoside hydrolase / ...Inosine-uridine preferring nucleoside hydrolase family protein / Nonspecific nucleoside hydrolase / Nonspecific_nucleoside_hydrolase/GeneDB:LmjF.18.1 580 / Nucleoside hydrolase


Mass: 34278.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote)
Gene: iunh, CGC20_39000, CGC21_5445, LdCL_180021000, LDHU3_18.2000
Production host: Escherichia coli (E. coli) / References: UniProt: Q8WQX2, purine nucleosidase

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Non-polymers , 6 types, 857 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 841 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 15% PEG 3350 0.1 M MES saturated hypoxanthine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019
RadiationMonochromator: Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 263968 / % possible obs: 94.1 % / Redundancy: 3.4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.057 / Net I/σ(I): 23.5
Reflection shellResolution: 1.73→1.76 Å / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6560 / CC1/2: 0.82 / Rpim(I) all: 0.264 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ezr

1ezr


Resolution: 1.73→25.87 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 20.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 8534 4.96 %
Rwork0.1739 --
obs0.1756 171940 62.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→25.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9351 0 81 841 10273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139693
X-RAY DIFFRACTIONf_angle_d1.32513226
X-RAY DIFFRACTIONf_dihedral_angle_d8.8091363
X-RAY DIFFRACTIONf_chiral_restr0.081584
X-RAY DIFFRACTIONf_plane_restr0.011686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.750.29241460.22332959X-RAY DIFFRACTION34
1.75-1.770.26511950.21533240X-RAY DIFFRACTION38
1.77-1.790.24621740.20113316X-RAY DIFFRACTION37
1.79-1.810.23991690.19633059X-RAY DIFFRACTION35
1.81-1.840.23262030.20223617X-RAY DIFFRACTION41
1.84-1.860.26172310.19474000X-RAY DIFFRACTION46
1.86-1.890.25562010.19164115X-RAY DIFFRACTION47
1.89-1.920.24141940.18184166X-RAY DIFFRACTION47
1.92-1.950.21941870.19254271X-RAY DIFFRACTION49
1.95-1.980.2311710.19624381X-RAY DIFFRACTION49
1.98-2.010.25552610.18854306X-RAY DIFFRACTION49
2.01-2.050.21992460.18114329X-RAY DIFFRACTION50
2.05-2.090.21972230.18234503X-RAY DIFFRACTION51
2.09-2.130.23092580.1784486X-RAY DIFFRACTION52
2.13-2.180.2352300.17824472X-RAY DIFFRACTION51
2.18-2.230.22192630.18065057X-RAY DIFFRACTION58
2.23-2.280.21012770.17385641X-RAY DIFFRACTION64
2.28-2.350.20652890.1756116X-RAY DIFFRACTION69
2.35-2.420.20442470.1786569X-RAY DIFFRACTION74
2.42-2.490.25023560.18037044X-RAY DIFFRACTION80
2.49-2.580.23363720.1827399X-RAY DIFFRACTION84
2.58-2.690.21553540.18017501X-RAY DIFFRACTION85
2.69-2.810.21093630.1786752X-RAY DIFFRACTION77
2.81-2.950.2293900.18017586X-RAY DIFFRACTION86
2.96-3.140.21554950.18177766X-RAY DIFFRACTION89
3.14-3.380.20764180.187553X-RAY DIFFRACTION87
3.38-3.720.21074060.17877305X-RAY DIFFRACTION83
3.72-4.260.18433520.15916551X-RAY DIFFRACTION75
4.26-5.360.17423770.14247722X-RAY DIFFRACTION87
5.36-25.870.15894860.16087624X-RAY DIFFRACTION88
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)
10.01520.00770.00110.0049-0.00710.00840.03070.0243-0.02740.02-0.0081-0.01040.0151-0.0233-0-0.04960.02220.09880.0420.0108-0.06758.5656-18.86150.6247
20.01340.0106-0.00550.0009-0.01380.00070.00070.011-0.04360.0499-0.0744-0.0799-0.02260.0001-0-0.0973-0.14460.071-0.09720.12390.038746.2129-13.674215.3629
30.0021-0.00550.00640.0017-0.01630.0033-0.07820.0083-0.07940.0145-0.0587-0.090.00430.0217-00.03460.0457-0.1372-0.03640.1921-0.070636.0989-46.399542.3535
40.00570.0041-0.00570.0082-0.00380.0091-0.0349-0.00220.06020.0540.0140.1025-0.04010.002700.0951-0.01080.04190.0379-0.0103-0.0044-1.9846-32.857840.7897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 313)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 314)
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 313)
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 313)

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