[English] 日本語
Yorodumi
- PDB-1lx7: Structure of E. coli uridine phosphorylase at 2.0A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lx7
TitleStructure of E. coli uridine phosphorylase at 2.0A
Componentsuridine phosphorylase
KeywordsTRANSFERASE / Structural genomics / UDRPase / P12758 / phosphorylase / nucleotide metabolism / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


UMP catabolic process / uridine catabolic process / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / potassium ion binding / DNA damage response / protein-containing complex / ATP binding / identical protein binding / 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
Uridine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBurling, T. / Buglino, J.A. / Kniewel, R. / Chadna, T. / Beckwith, A. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of Escherichia coli uridine phosphorylase at 2.0 A.
Authors: Burling, F.T. / Kniewel, R. / Buglino, J.A. / Chadha, T. / Beckwith, A. / Lima, C.D.
History
DepositionJun 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: uridine phosphorylase
B: uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)55,1282
Polymers55,1282
Non-polymers00
Water6,503361
1
A: uridine phosphorylase
B: uridine phosphorylase

A: uridine phosphorylase
B: uridine phosphorylase

A: uridine phosphorylase
B: uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)165,3856
Polymers165,3856
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area15600 Å2
ΔGint-116 kcal/mol
Surface area48520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)151.375, 151.375, 48.151
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein uridine phosphorylase / UDRPase


Mass: 27564.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: T7 expression system / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: P12758, uridine phosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Mes, 10% PEG 4K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1droppH8.
350 mM1dropNaCl
41 mMdithiothreitol1drop
510 %PEG40001reservoir
60.1 MMES1reservoirpH6.5
75 %glycerol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9794 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 76551 / Num. obs: 55347 / % possible obs: 72.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.032
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.135 / % possible all: 54.5
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. obs: 49742 / % possible obs: 89.2 % / Num. measured all: 747216 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 78.6 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 15.6

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.9refinement
RefinementMethod to determine structure: SAD / Resolution: 2→19.67 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1315 5 %RANDOM
Rwork0.182 ---
all-29610 --
obs-26441 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.336 Å2 / ksol: 0.34852 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.97 Å2-1.88 Å20 Å2
2---5.97 Å20 Å2
3---11.94 Å2
Refine analyzeLuzzati coordinate error free: 0.24 Å / Luzzati sigma a free: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 0 361 3873
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.262
X-RAY DIFFRACTIONc_mcangle_it1.942.5
X-RAY DIFFRACTIONc_scbond_it2.342.5
X-RAY DIFFRACTIONc_scangle_it3.123
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 174 4.3 %
Rwork0.204 3906 -
obs--87.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 4.7 % / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor obs: 0.204

+
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