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- PDB-6zk5: Plant nucleoside hydrolase - ZmNRh3 enzyme in complex with forodesine -

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Basic information

Entry
Database: PDB / ID: 6zk5
TitlePlant nucleoside hydrolase - ZmNRh3 enzyme in complex with forodesine
ComponentsNucleoside N-ribohydrolase 3
KeywordsHYDROLASE / Plant enzyme
Function / homology
Function and homology information


: / hydrolase activity, hydrolyzing N-glycosyl compounds / nucleobase-containing compound metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / metal ion binding
Similarity search - Function
Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like
Similarity search - Domain/homology
Chem-IMH / TRIETHYLENE GLYCOL / Nucleoside N-ribohydrolase 3
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMorera, S. / Vigouroux, A. / Kopecny, D.
CitationJournal: Plant J. / Year: 2023
Title: Plant nucleoside N-ribohydrolases: riboside binding and role in nitrogen storage mobilization.
Authors: Luptakova, E. / Vigouroux, A. / Koncitikova, R. / Kopecna, M. / Zalabak, D. / Novak, O. / Salcedo Sarmiento, S. / Cavar Zeljkovic, S. / Kopecny, D.J. / von Schwartzenberg, K. / Strnad, M. / ...Authors: Luptakova, E. / Vigouroux, A. / Koncitikova, R. / Kopecna, M. / Zalabak, D. / Novak, O. / Salcedo Sarmiento, S. / Cavar Zeljkovic, S. / Kopecny, D.J. / von Schwartzenberg, K. / Strnad, M. / Spichal, L. / De Diego, N. / Kopecny, D. / Morera, S.
History
DepositionJun 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside N-ribohydrolase 3
B: Nucleoside N-ribohydrolase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4699
Polymers71,5822
Non-polymers8877
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-33 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.540, 79.270, 85.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nucleoside N-ribohydrolase 3 / Pyrimidine-specific ribonucleoside hydrolase rihB


Mass: 35790.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100282231, NRH3, ZEAMMB73_Zm00001d005343 / Production host: Escherichia coli (E. coli)
References: UniProt: B6T563, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 5 types, 309 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-IMH / 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL / Forodesine / Immucillin H


Mass: 266.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N4O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→42.61 Å / Num. obs: 42550 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→2.01 Å / Num. unique obs: 6773 / CC1/2: 0.572

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KPO

4kpo


Resolution: 1.9→42.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.162 / SU Rfree Blow DPI: 0.129 / SU Rfree Cruickshank DPI: 0.128
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2128 5 %RANDOM
Rwork0.17 ---
obs0.171 42550 99.9 %-
Displacement parametersBiso max: 123.03 Å2 / Biso mean: 36.43 Å2 / Biso min: 19.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.3798 Å20 Å20 Å2
2---2.9043 Å20 Å2
3---1.5245 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.9→42.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 58 302 5172
Biso mean--32.25 39.9 -
Num. residues----632
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1651SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes852HARMONIC5
X-RAY DIFFRACTIONt_it4985HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion670SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6221SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4985HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6794HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion17.04
LS refinement shellResolution: 1.9→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2999 43 5.05 %
Rwork0.2543 808 -
all0.2566 851 -
obs--96.03 %
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)
10.7493-0.00340.17870.6074-0.15841.2216-0.03070.0118-0.0045-0.00430.0141-0.0014-0.0598-0.15860.0166-0.0560.0145-0.0031-0.0585-0.0172-0.0414-17.6182-2.5265-0.3337
22.23390.4464-0.82580.641-0.27151.05870.1389-0.06650.12020.0685-0.07440.0672-0.07410.0488-0.0646-0.0729-0.00830.0067-0.07690.0113-0.079619.75943.1544-18.0551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 315
2X-RAY DIFFRACTION2{ B|* }B0 - 315

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