[English] 日本語
Yorodumi
- PDB-1ryz: Uridine Phosphorylase from Salmonella typhimurium. Crystal Struct... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ryz
TitleUridine Phosphorylase from Salmonella typhimurium. Crystal Structure at 2.9 A Resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylase / nucleoside phosphorylase
Function / homology
Function and homology information


nucleotide catabolic process / deoxyuridine phosphorylase activity / uridine phosphorylase / nucleoside catabolic process / uridine phosphorylase activity / UMP salvage / cytosol
Similarity search - Function
Uridine phosphorylase / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Uridine phosphorylase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDontsova, M.V. / Gabdoulkhakov, A.G. / Lyashenko, A.V. / Nikonov, S.V. / Ealick, S.E. / Mikhailov, A.M.
CitationJournal: TO BE PUBLISHED
Title: Structure-functions studies of uridine phosphorylase from Salmonella typhimurium
Authors: Dontsova, M.V. / Gabdoulkhakov, A.G. / Lyashenko, A.V. / Nikonov, S.V. / Ealick, S.E. / Mikhailov, A.M.
History
DepositionDec 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Uridine phosphorylase
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
E: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,1358
Polymers163,0156
Non-polymers1202
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Uridine phosphorylase
E: Uridine phosphorylase

A: Uridine phosphorylase
B: Uridine phosphorylase
D: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,1358
Polymers163,0156
Non-polymers1202
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
identity operation1_555x,y,z1
Buried area18280 Å2
ΔGint-108 kcal/mol
Surface area51990 Å2
MethodPISA
3
B: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4584
Polymers54,3382
Non-polymers1202
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
C: Uridine phosphorylase
E: Uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)54,3382
Polymers54,3382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.260, 92.260, 267.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein
Uridine phosphorylase / UrdPase / UPase


Mass: 27169.092 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: udp / Plasmid: pBluescript IISK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A1F6, uridine phosphorylase
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Na Acetate trihydrate, 10% PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2003 / Details: Capillary optics
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 75053 / Num. obs: 26462 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.84 % / Biso Wilson estimate: -0.2 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.177 / Net I/σ(I): 6.89
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.79 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.05 / Num. unique all: 1074 / Rsym value: 0.333 / % possible all: 75.9

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K3F

1k3f


Resolution: 2.9→29.46 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3363606.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1327 5 %RANDOM
Rwork0.212 ---
all0.216 ---
obs0.212 26462 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.0393 Å2 / ksol: 0.301264 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11262 0 8 0 11270
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it7.941.5
X-RAY DIFFRACTIONc_mcangle_it11.792
X-RAY DIFFRACTIONc_scbond_it10.412
X-RAY DIFFRACTIONc_scangle_it13.922.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 198 4.7 %
Rwork0.211 3979 -
obs-3979 88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ACY_XPLOR.PARAMACY_XPLOR.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

+
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