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- PDB-1mp5: Y177F VARIANT OF S. ENTERICA RmlA -

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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 / extracellular polysaccharide 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water0
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

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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 / Uridine diphosphate glucose


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

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Experimental details

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Experiment

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

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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

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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

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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

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