[English] 日本語
Yorodumi
- PDB-4kpn: Plant nucleoside hydrolase - PpNRh1 enzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kpn
TitlePlant nucleoside hydrolase - PpNRh1 enzyme
ComponentsNucleoside N-ribohydrolase 1
KeywordsHYDROLASE / IU-NRHs
Function / homology
Function and homology information


purine nucleosidase / purine nucleosidase activity / purine nucleoside catabolic process / metal ion binding / cytosol
Similarity search - Function
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
Nucleoside N-ribohydrolase 1 / Nucleoside N-ribohydrolase 1
Similarity search - Component
Biological speciesPhyscomitrella patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsMorera, S. / Vigouroux, A. / Kopecny, D.
CitationJournal: Plant Physiol. / Year: 2013
Title: Structure and Function of Nucleoside Hydrolases from Physcomitrella patens and Maize Catalyzing the Hydrolysis of Purine, Pyrimidine, and Cytokinin Ribosides.
Authors: Kopecna, M. / Blaschke, H. / Kopecny, D. / Vigouroux, A. / Koncitikova, R. / Novak, O. / Kotland, O. / Strnad, M. / Morera, S. / von Schwartzenberg, K.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2May 7, 2014Group: Other
Revision 1.3Sep 20, 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 / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoside N-ribohydrolase 1
B: Nucleoside N-ribohydrolase 1
C: Nucleoside N-ribohydrolase 1
D: Nucleoside N-ribohydrolase 1
E: Nucleoside N-ribohydrolase 1
F: Nucleoside N-ribohydrolase 1
G: Nucleoside N-ribohydrolase 1
H: Nucleoside N-ribohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,11516
Polymers299,7948
Non-polymers3218
Water28816
1
A: Nucleoside N-ribohydrolase 1
B: Nucleoside N-ribohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0294
Polymers74,9492
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-43 kcal/mol
Surface area23710 Å2
MethodPISA
2
C: Nucleoside N-ribohydrolase 1
D: Nucleoside N-ribohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0294
Polymers74,9492
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-42 kcal/mol
Surface area24080 Å2
MethodPISA
3
E: Nucleoside N-ribohydrolase 1
F: Nucleoside N-ribohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0294
Polymers74,9492
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-41 kcal/mol
Surface area23920 Å2
MethodPISA
4
G: Nucleoside N-ribohydrolase 1
H: Nucleoside N-ribohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0294
Polymers74,9492
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-42 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.850, 126.080, 253.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Nucleoside N-ribohydrolase 1


Mass: 37474.277 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrella patens (plant) / Gene: NRH1 / Production host: Escherichia coli (E. coli)
References: UniProt: M1FQT3, UniProt: A9TXA6*PLUS, purine nucleosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Hepes, 100mM sodium acetate, 10% PEG4K, 10%EG, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2011
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.35→44.7 Å / Num. all: 59000 / Num. obs: 58554 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 73.44 Å2
Reflection shellResolution: 3.35→3.55 Å / % possible all: 98

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3B9X

3b9x


Resolution: 3.35→38.68 Å / Cor.coef. Fo:Fc: 0.9191 / Cor.coef. Fo:Fc free: 0.9093 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 2927 5 %RANDOM
Rwork0.2034 ---
obs0.2039 58532 99.62 %-
all-59000 --
Displacement parametersBiso mean: 97.07 Å2
Baniso -1Baniso -2Baniso -3
1--3.2163 Å20 Å20 Å2
2--4.8666 Å20 Å2
3----1.6503 Å2
Refine analyzeLuzzati coordinate error obs: 0.715 Å
Refinement stepCycle: LAST / Resolution: 3.35→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19496 0 8 16 19520
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00819952HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1227240HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6584SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes472HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2912HARMONIC5
X-RAY DIFFRACTIONt_it19952HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion23.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2744SEMIHARMONIC5
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_contact24602SEMIHARMONIC4
LS refinement shellResolution: 3.35→3.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2451 209 5.01 %
Rwork0.2561 3963 -
all0.2555 4172 -
obs--99.62 %
Refinement TLS params.Method: refined / Origin x: 15.5819 Å / Origin y: -16.4845 Å / Origin z: -35.8124 Å
111213212223313233
T-0.1453 Å2-0.0973 Å2-0.0329 Å2--0.0705 Å20.0111 Å2---0.1804 Å2
L0.4212 °2-0.1685 °20.0067 °2-0.6452 °2-0.1056 °2--0.5014 °2
S0.03 Å °-0.0549 Å °-0.0169 Å °-0.0829 Å °0.0678 Å °-0.0315 Å °-0.0742 Å °0.1031 Å °-0.0979 Å °
Refinement TLS groupSelection details: { *|* }

+
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