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- PDB-3juj: The crystal structure of apo- UDP-glucose pyrophosphorylase -

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Basic information

Entry
Database: PDB / ID: 3juj
TitleThe crystal structure of apo- UDP-glucose pyrophosphorylase
ComponentsUDP-glucose pyrophosphorylase (GalU)
KeywordsTRANSFERASE / UDP-glucose pyrophosphorylase / Helicobacter pylori
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / biosynthetic process
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 speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsKim, H. / Kim, K.K.
CitationJournal: Mol.Cells / Year: 2010
Title: Structural basis for the reaction mechanism of UDP-glucose pyrophosphorylase
Authors: Kim, H. / Choi, J. / Kim, T. / Lokanath, N.K. / Ha, S.C. / Suh, S.W. / Hwang, H.-Y. / Kim, K.K.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glucose pyrophosphorylase (GalU)
B: UDP-glucose pyrophosphorylase (GalU)
C: UDP-glucose pyrophosphorylase (GalU)
D: UDP-glucose pyrophosphorylase (GalU)


Theoretical massNumber of molelcules
Total (without water)128,3484
Polymers128,3484
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-64 kcal/mol
Surface area43000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.466, 98.614, 245.700
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
UDP-glucose pyrophosphorylase (GalU)


Mass: 32086.932 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0646 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli)
References: UniProt: O25363, UTP-glucose-1-phosphate uridylyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.32 Å3/Da / Density % sol: 71.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate trihydrate, 2M ammonium sulfate, 0.1M guanidine HCl, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL38B111
SYNCHROTRONSPring-8 BL38B120.9791, 0.9794, 0.9840
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDDec 4, 2003
ADSC QUANTUM 4r2CCDDec 4, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97911
30.97941
40.9841
ReflectionResolution: 2.9→50 Å / Num. all: 50147 / Num. obs: 47890 / % possible obs: 95.5 % / Biso Wilson estimate: 4.4 Å2 / Rsym value: 0.077 / Net I/σ(I): 19.4
Reflection shellResolution: 2.9→3 Å / Num. unique all: 4638 / Rsym value: 0.31 / % possible all: 94

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2263 4.5 %RANDOM
Rwork0.225 42936 --
obs-45199 90.2 %-
Solvent computationBsol: 34.508 Å2
Displacement parametersBiso max: 133.48 Å2 / Biso mean: 57.904 Å2 / Biso min: 13.28 Å2
Baniso -1Baniso -2Baniso -3
1--39.3 Å20 Å20 Å2
2--23.452 Å20 Å2
3---15.848 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8688 0 0 95 8783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.493
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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