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- PDB-2e3d: Crystal structure of E. coli glucose-1-phosphate uridylyltransferase -

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Basic information

Entry
Database: PDB / ID: 2e3d
TitleCrystal structure of E. coli glucose-1-phosphate uridylyltransferase
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / UDP-glucose / carbohydrate / pyrophosphorylase
Function / homology
Function and homology information


osmoregulated periplasmic glucan biosynthetic process / colanic acid biosynthetic process / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / galactose catabolic process via UDP-galactose / UDP-glucose metabolic process / lipopolysaccharide core region biosynthetic process / protein homotetramerization / magnesium ion binding / identical protein binding / cytosol
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase, bacterial/archaeal-type / 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
UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIR / Resolution: 1.95 Å
AuthorsThoden, J.B. / Holden, H.M.
CitationJournal: Protein Sci. / Year: 2007
Title: The molecular architecture of glucose-1-phosphate uridylyltransferase
Authors: Thoden, J.B. / Holden, H.M.
History
DepositionNov 22, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
C: UTP--glucose-1-phosphate uridylyltransferase
D: UTP--glucose-1-phosphate uridylyltransferase


Theoretical massNumber of molelcules
Total (without water)131,9214
Polymers131,9214
Non-polymers00
Water14,160786
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12460 Å2
ΔGint-100 kcal/mol
Surface area44250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.900, 109.300, 100.500
Angle α, β, γ (deg.)90.000, 93.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
UTP--glucose-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase / UDPGP / Alpha-D-glucosyl-1-phosphate uridylyltransferase / Uridine ...UDP-glucose pyrophosphorylase / UDPGP / Alpha-D-glucosyl-1-phosphate uridylyltransferase / Uridine diphosphoglucose pyrophosphorylase


Mass: 32980.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12/W3110 / Gene: galU / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: P0AEP3, UTP-glucose-1-phosphate uridylyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 786 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.0 M ammomium sulfate, 0.2M lithium chloride, 0.1M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 12, 2006 / Details: Montel
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 106815 / Num. obs: 106815 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.076 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 7817 / Rsym value: 0.372 / % possible all: 96.5

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Processing

Software
NameVersionClassificationNB
TNTrefinement
PDB_EXTRACT2data extraction
PROTEUM PLUSdata collection
SAINTdata reduction
SADABSdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIR / Resolution: 1.95→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 10623 -random
Rwork0.198 ---
all0.202 106815 --
obs0.202 106815 98.5 %-
Displacement parametersBiso mean: 31.584 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8656 0 0 786 9442
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.5
X-RAY DIFFRACTIONt_bond_d0.014

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