[English] 日本語
Yorodumi
- PDB-6zk2: Plant nucleoside hydrolase - ZmNRh2b in complex with forodesine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zk2
TitlePlant nucleoside hydrolase - ZmNRh2b in complex with forodesine
ComponentsPyrimidine-specific ribonucleoside hydrolase rihA
KeywordsHYDROLASE / plant enzyme
Function / homology
Function and homology information


uridine nucleosidase / 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
Chem-IMH / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / uridine nucleosidase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)151,94642
Polymers148,4894
Non-polymers3,45638
Water9,800544
1
A: Pyrimidine-specific ribonucleoside hydrolase rihA
B: Pyrimidine-specific ribonucleoside hydrolase rihA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,14123
Polymers74,2452
Non-polymers1,89621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-7 kcal/mol
Surface area24300 Å2
MethodPISA
2
C: Pyrimidine-specific ribonucleoside hydrolase rihA
D: Pyrimidine-specific ribonucleoside hydrolase rihA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,80519
Polymers74,2452
Non-polymers1,56017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-24 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.920, 148.980, 88.510
Angle α, β, γ (deg.)90.000, 102.400, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
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

-
Non-polymers , 7 types, 582 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C11H14N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4000, Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→46.8 Å / Num. obs: 59871 / % possible obs: 97.6 % / Redundancy: 3.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.163 / Net I/σ(I): 6.4
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 5446 / CC1/2: 0.827

-
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: 2.2→30.12 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.314 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.211
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2993 5 %RANDOM
Rwork0.191 ---
obs0.193 59859 97.6 %-
Displacement parametersBiso max: 144.75 Å2 / Biso mean: 43.94 Å2 / Biso min: 12.98 Å2
Baniso -1Baniso -2Baniso -3
1--6.5544 Å20 Å2-6.5612 Å2
2--3.3653 Å20 Å2
3---3.1891 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.2→30.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9608 0 212 544 10364
Biso mean--49 41.56 -
Num. residues----1264
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3354SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1708HARMONIC5
X-RAY DIFFRACTIONt_it10022HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1324SEMIHARMONIC5
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_contact11637SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10022HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13572HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion16.82
LS refinement shellResolution: 2.2→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.293 60 5.01 %
Rwork0.2466 1138 -
all0.2489 1198 -
obs--64.43 %
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)
10.88020.1215-0.41830.5388-0.21242.7598-0.0638-0.1008-0.082-0.0309-0.0303-0.00630.14980.1390.0942-0.11590.0282-0.0288-0.02920.0154-0.093813.08520.099715.5846
20.774-0.0237-0.85880.6721-0.00512.9379-0.10220.1713-0.0579-0.0735-0.03330.01420.3521-0.3910.1355-0.0837-0.0542-0.0287-0.037-0.0173-0.13337.99011.7779-26.4631
31.82720.3092-0.62541.7086-1.24872.57650.4178-0.34630.29230.7157-0.13810.1089-0.88210.2359-0.27970.0805-0.15890.1347-0.2509-0.1038-0.211923.711437.54960.4469
41.13190.7283-0.47511.6897-0.77252.82750.03440.17470.2756-0.140.08370.0663-0.3389-0.0627-0.1181-0.14240.03820.0204-0.11810.0698-0.072226.943837.7535-41.5988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A10 - 325
2X-RAY DIFFRACTION2{ B|* }B10 - 325
3X-RAY DIFFRACTION3{ C|* }C10 - 325
4X-RAY DIFFRACTION4{ D|* }D10 - 325

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more