[English] 日本語
Yorodumi
- PDB-1mp5: Y177F VARIANT OF S. ENTERICA RmlA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mp5
TitleY177F VARIANT OF S. ENTERICA RmlA
ComponentsY177F VARIANT OF S. ENTERICA RmlA BOUND TO UDP-GLUCOSE
KeywordsTRANSFERASE
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / biosynthetic process / nucleotide binding / magnesium ion binding / metal ion binding
Similarity search - Function
Glucose-1-phosphate thymidylyltransferase, short form / Nucleotidyl transferase domain / Nucleotidyl transferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glucose-1-phosphate thymidylyltransferase / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBarton, W.A. / Biggins, J.B. / Jiang, J. / Thorson, J.S. / Nikolov, D.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Expanding pyrimidine diphosphosugar libraries via structure-based nucleotidylyltransferase engineering
Authors: Barton, W.A. / Biggins, J.B. / Jiang, J. / Thorson, J.S. / Nikolov, D.B.
History
DepositionSep 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / 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_database_remark.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Author states the sequence of the deposited model differs from the published sequence, ...SEQUENCE Author states the sequence of the deposited model differs from the published sequence, because there are confirmed natural mutations in the variant of Salmonella used in this entry.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Y177F VARIANT OF S. ENTERICA RmlA BOUND TO UDP-GLUCOSE
B: Y177F VARIANT OF S. ENTERICA RmlA BOUND TO UDP-GLUCOSE
C: Y177F VARIANT OF S. ENTERICA RmlA BOUND TO UDP-GLUCOSE
D: Y177F VARIANT OF S. ENTERICA RmlA BOUND TO UDP-GLUCOSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,9108
Polymers129,6444
Non-polymers2,2654
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13610 Å2
ΔGint-70 kcal/mol
Surface area42010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.700, 111.220, 131.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Y177F VARIANT OF S. ENTERICA RmlA BOUND TO UDP-GLUCOSE / Thymidylyltransferase


Mass: 32411.100 Da / Num. of mol.: 4 / Mutation: Y177F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9F7G8, UniProt: P26393*PLUS, glucose-1-phosphate thymidylyltransferase
#2: Chemical
ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24N2O17P2

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growpH: 7 / Details: pH 7.0, temperature 100K
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115-20 mg/mlprotein1drop
210 mM1dropKCl
35 mMHEPES1droppH7.4
41.8-1.9 Mammonium sulfate1reservoir
55-7.5 %(v/v)isopropanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1395 Å
DetectorDate: Jun 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1395 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 43514 / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.75 Å / % possible obs: 98.3 % / Redundancy: 5 % / Rmerge(I) obs: 0.061

-
Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IIN

1iin


Resolution: 2.75→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh&Huber
RfactorNum. reflectionSelection details
Rfree0.29 3486 RANDOM
Rwork0.23 --
all-35556 -
obs-34202 -
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9041 0 144 0 9185
Refinement
*PLUS
Lowest resolution: 8 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.009
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.34

+
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