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- PDB-6zk4: Plant nucleoside hydrolase - ZmNRh2b with a bound adenine -

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Basic information

Entry
Database: PDB / ID: 6zk4
TitlePlant nucleoside hydrolase - ZmNRh2b with a bound adenine
ComponentsPyrimidine-specific ribonucleoside hydrolase rihA
KeywordsHYDROLASE / Plant enzyme
Function / homology
Function and homology information


purine nucleosidase activity / purine nucleoside catabolic process / metal ion binding / cytosol
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
ADENINE / DI(HYDROXYETHYL)ETHER / Pyrimidine-specific ribonucleoside hydrolase rihA
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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

Downloads & links

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Assembly

Deposited unit
A: Pyrimidine-specific ribonucleoside hydrolase rihA
B: Pyrimidine-specific ribonucleoside hydrolase rihA
C: Pyrimidine-specific ribonucleoside hydrolase rihA
D: Pyrimidine-specific ribonucleoside hydrolase rihA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,46415
Polymers148,4894
Non-polymers97511
Water9,368520
1
A: Pyrimidine-specific ribonucleoside hydrolase rihA
B: Pyrimidine-specific ribonucleoside hydrolase rihA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8078
Polymers74,2452
Non-polymers5636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-27 kcal/mol
Surface area23610 Å2
MethodPISA
2
C: Pyrimidine-specific ribonucleoside hydrolase rihA
D: Pyrimidine-specific ribonucleoside hydrolase rihA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6577
Polymers74,2452
Non-polymers4125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-31 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.640, 148.180, 88.410
Angle α, β, γ (deg.)90.000, 102.710, 90.000
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
Pyrimidine-specific ribonucleoside hydrolase rihA


Mass: 37122.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 542168, ZEAMMB73_Zm00001d031958 / Production host: Escherichia coli (E. coli) / References: UniProt: B6THD4

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Non-polymers , 5 types, 531 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, Tris

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.95→42.86 Å / Num. obs: 86204 / % possible obs: 98.5 % / Redundancy: 3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.4
Reflection shellResolution: 1.95→2.06 Å / Num. unique obs: 13693 / CC1/2: 0.628

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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: 1.95→42.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.137
RfactorNum. reflection% reflectionSelection details
Rfree0.203 4299 5 %RANDOM
Rwork0.175 ---
obs0.177 85979 99 %-
Displacement parametersBiso max: 153.38 Å2 / Biso mean: 50.74 Å2 / Biso min: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.9489 Å20 Å2-2.0641 Å2
2--5.3976 Å20 Å2
3---2.5513 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.95→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9610 0 72 520 10202
Biso mean--57.34 46.73 -
Num. residues----1266
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3312SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1720HARMONIC5
X-RAY DIFFRACTIONt_it9909HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1311SEMIHARMONIC5
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_contact11748SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9909HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13456HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion16.4
LS refinement shellResolution: 1.95→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2881 86 5 %
Rwork0.2516 1634 -
all0.2534 1720 -
obs--98.08 %
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)
10.73990.0523-0.07660.4967-0.13881.6096-0.0366-0.0662-0.1345-0.02550.00110.0020.09390.0790.0354-0.14380.0339-0.0176-0.14570.0184-0.145450.55220.300158.7779
20.69830.0563-0.47631.0756-0.28132.5919-0.05080.1364-0.0817-0.13890.0033-0.01820.4047-0.25360.0475-0.1125-0.033-0.0165-0.1767-0.0296-0.197145.482.080316.8197
31.11670.1583-0.09322.7077-1.27681.98370.0949-0.15920.12930.8145-0.0706-0.158-0.62120.027-0.02430.0542-0.0424-0.0204-0.2697-0.0349-0.257661.267637.655143.6149
41.02591.01870.01653.0403-0.89633.3402-0.15820.14680.1416-0.60470.0199-0.1321-0.22310.26010.1383-0.1416-0.00690.0437-0.23820.0372-0.233964.987337.73111.5036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A10 - 325
2X-RAY DIFFRACTION2{ B|* }B9 - 325
3X-RAY DIFFRACTION3{ C|* }C9 - 325
4X-RAY DIFFRACTION4{ D|* }D10 - 325

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