[English] 日本語
Yorodumi
- PDB-3euf: Crystal structure of BAU-bound human uridine phosphorylase 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3euf
TitleCrystal structure of BAU-bound human uridine phosphorylase 1
ComponentsUridine phosphorylase 1
KeywordsTRANSFERASE / nucleoside phosphorylase / uridine rescue / 5-benzylacyclouridine / Alternative splicing / Glycosyltransferase
Function / homology
Function and homology information


CMP catabolic process / dTMP catabolic process / dCMP catabolic process / thymidine phosphorylase activity / UMP catabolic process / dUMP catabolic process / uridine catabolic process / Pyrimidine catabolism / Pyrimidine salvage / deoxyuridine phosphorylase activity ...CMP catabolic process / dTMP catabolic process / dCMP catabolic process / thymidine phosphorylase activity / UMP catabolic process / dUMP catabolic process / uridine catabolic process / Pyrimidine catabolism / Pyrimidine salvage / deoxyuridine phosphorylase activity / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / nucleobase-containing compound metabolic process / cellular response to glucose starvation / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Uridine phosphorylase, eukaryotic / 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
Chem-BAU / PHOSPHATE ION / Uridine phosphorylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRoosild, T.P.
CitationJournal: Bmc Struct.Biol. / Year: 2009
Title: Implications of the structure of human uridine phosphorylase 1 on the development of novel inhibitors for improving the therapeutic window of fluoropyrimidine chemotherapy.
Authors: Roosild, T.P. / Castronovo, S. / Fabbiani, M. / Pizzorno, G.
History
DepositionOct 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Uridine phosphorylase 1
B: Uridine phosphorylase 1
C: Uridine phosphorylase 1
D: Uridine phosphorylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,68812
Polymers144,2024
Non-polymers1,4858
Water6,053336
1
A: Uridine phosphorylase 1
B: Uridine phosphorylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8446
Polymers72,1012
Non-polymers7434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-25.8 kcal/mol
Surface area22470 Å2
MethodPISA
2
C: Uridine phosphorylase 1
D: Uridine phosphorylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8446
Polymers72,1012
Non-polymers7434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-23.2 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.197, 74.442, 262.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A79 - 84
2115B79 - 84
3115C79 - 84
4115D79 - 84
1125A308 - 309
2125D308 - 309

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Uridine phosphorylase 1 / UrdPase 1 / UPase 1


Mass: 36050.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UPP1, UP / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16831, uridine phosphorylase
#2: Chemical
ChemComp-BAU / 1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE


Mass: 276.288 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16N2O4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG 3350, 300mM KCl, 30mM MgCl2, 100mM Bis-Tris Buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 103357 / Num. obs: 103213 / % possible obs: 99.8 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 100 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2 / Num. unique all: 10192 / Num. unique obs: 10192 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U1C

1u1c


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.403 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25147 5155 5 %RANDOM
Rwork0.2024 ---
obs0.20481 97957 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.999 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.81 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9030 0 100 336 9466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0229278
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.99212526
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97251170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70723.656372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.157151648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2441564
X-RAY DIFFRACTIONr_chiral_restr0.1120.21434
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026836
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.24028
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.26427
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2417
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4120.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2681.56025
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9129380
X-RAY DIFFRACTIONr_scbond_it3.02433713
X-RAY DIFFRACTIONr_scangle_it4.5244.53146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A24medium positional0.440.5
12B24medium positional0.310.5
13C24medium positional0.310.5
14D24medium positional0.310.5
21A4medium positional0.090.5
11A20loose positional0.975
12B20loose positional0.685
13C20loose positional0.95
14D20loose positional0.885
21A2loose positional0.155
11A24medium thermal2.892
12B24medium thermal2.62
13C24medium thermal2.362
14D24medium thermal2.112
21A4medium thermal0.562
11A20loose thermal3.4910
12B20loose thermal2.7110
13C20loose thermal3.6710
14D20loose thermal3.2910
21A2loose thermal0.1810
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 386 -
Rwork0.276 7117 -
obs--99.67 %

+
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