[English] 日本語
Yorodumi
- PDB-1yoe: Crystal structure of a the E. coli pyrimidine nucleoside hydrolas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yoe
TitleCrystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose
ComponentsHypothetical protein ybeK
KeywordsHYDROLASE / Pyrimidine nucleoside hydrolase / bacterial nucleosidase / ribose / enzyme-product complex
Function / homology
Function and homology information


ribosylpyrimidine nucleosidase activity / pyrimidine ribonucleoside catabolic process / Hydrolases; Glycosylases / uridine nucleosidase activity / purine nucleosidase activity / pyrimidine nucleobase metabolic process / nucleobase-containing small molecule interconversion / purine nucleoside catabolic process / protein homotetramerization / calcium ion binding ...ribosylpyrimidine nucleosidase activity / pyrimidine ribonucleoside catabolic process / Hydrolases; Glycosylases / uridine nucleosidase activity / purine nucleosidase activity / pyrimidine nucleobase metabolic process / nucleobase-containing small molecule interconversion / purine nucleoside catabolic process / protein homotetramerization / calcium ion binding / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Pyrimidine-specific ribonucleoside hydrolase RihA / 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
alpha-D-ribofuranose / Pyrimidine-specific ribonucleoside hydrolase RihA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsMuzzolini, L. / Versees, W. / Steyaert, J. / Degano, M.
Citation
Journal: To be Published
Title: Crystal structure of the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose
Authors: Muzzolini, L. / Versees, W. / Steyaert, J. / Degano, M.
#1: Journal: Structure / Year: 2004
Title: Crystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy
Authors: Giabbai, B. / Degano, M.
#2: Journal: J.Mol.Biol. / Year: 2001
Title: Structure and function of a novel purine specific nucleoside hydrolase from Trypanosoma vivax
Authors: Versees, W. / Decanniere, K. / Pelle, R. / Depoorter, J. / Brosens, E. / Parkin, D.W. / Steyaert, J.
#3: Journal: Biochemistry / Year: 1998
Title: Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor
Authors: Degano, M. / Almo, S.C. / Sacchettini, J.C. / Schramm, V.L.
History
DepositionJan 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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 / _pdbx_validate_chiral.auth_atom_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein ybeK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3183
Polymers35,1281
Non-polymers1902
Water3,873215
1
A: Hypothetical protein ybeK
hetero molecules

A: Hypothetical protein ybeK
hetero molecules

A: Hypothetical protein ybeK
hetero molecules

A: Hypothetical protein ybeK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,27312
Polymers140,5124
Non-polymers7618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
2
A: Hypothetical protein ybeK
hetero molecules

A: Hypothetical protein ybeK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6376
Polymers70,2562
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area10290 Å2
ΔGint-118 kcal/mol
Surface area41620 Å2
MethodPISA
3
A: Hypothetical protein ybeK
hetero molecules

A: Hypothetical protein ybeK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6376
Polymers70,2562
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area2640 Å2
ΔGint-38 kcal/mol
Surface area23320 Å2
MethodPISA
4
A: Hypothetical protein ybeK
hetero molecules

A: Hypothetical protein ybeK
hetero molecules

A: Hypothetical protein ybeK
hetero molecules

A: Hypothetical protein ybeK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,27312
Polymers140,5124
Non-polymers7618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)76.466, 84.062, 112.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Hypothetical protein ybeK


Mass: 35128.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ybeK/rihA / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 / References: UniProt: P41409, ribosylpyrimidine nucleosidase
#2: Sugar ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.6 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: MPD, Sodium Acetate, ribose, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.78→25 Å / Num. all: 34056 / Num. obs: 34056 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.116 / Net I/σ(I): 26.2
Reflection shellResolution: 1.78→1.86 Å / Mean I/σ(I) obs: 2.9 / Num. unique all: 2669 / Rsym value: 0.475 / % possible all: 77.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: YeiK PDB code 1Q8F

1q8f


Resolution: 1.78→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.818 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Individual + TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19276 1086 3.2 %RANDOM
Rwork0.16733 ---
all0.1681 34056 --
obs0.16811 34056 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.623 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2---0.79 Å20 Å2
3---0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.098 Å0.102 Å
Refinement stepCycle: LAST / Resolution: 1.78→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 11 215 2521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222399
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9753278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755301
X-RAY DIFFRACTIONr_chiral_restr0.0720.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021780
X-RAY DIFFRACTIONr_nbd_refined0.1910.21123
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2165
X-RAY DIFFRACTIONr_metal_ion_refined0.060.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.238
X-RAY DIFFRACTIONr_mcbond_it131516
X-RAY DIFFRACTIONr_mcangle_it1.74352467
X-RAY DIFFRACTIONr_scbond_it2.8627883
X-RAY DIFFRACTIONr_scangle_it4.61810811
LS refinement shellResolution: 1.785→1.831 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 64 -
Rwork0.192 1826 -
obs-1826 75.8 %
Refinement TLS params.Method: refined / Origin x: -4.433 Å / Origin y: 20.7639 Å / Origin z: 36.7434 Å
111213212223313233
T0.0052 Å2-0.0005 Å2-0.0056 Å2-0.0178 Å20.0012 Å2--0.0061 Å2
L0.1453 °20.0651 °20.0439 °2-0.3512 °20.0581 °2--0.1442 °2
S-0.0032 Å °0.0185 Å °0.0038 Å °-0.0295 Å °0.0249 Å °0.0211 Å °-0.0068 Å °0.0061 Å °-0.0217 Å °

+
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