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- PDB-3juk: The Crystal Structure of UDP-glucose pyrophosphorylase complexed ... -

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Basic information

Entry
Database: PDB / ID: 3juk
TitleThe Crystal Structure of UDP-glucose pyrophosphorylase complexed with UDP-glucose
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
URIDINE-5'-DIPHOSPHATE-GLUCOSE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,90520
Polymers128,3484
Non-polymers2,55716
Water13,259736
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.444, 74.393, 167.123
Angle α, β, γ (deg.)90.00, 97.91, 90.00
Int Tables number5
Space group name H-MC121

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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: 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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 736 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-Na pH 7.5, 2% PEG 400, 1.5M ammonium sulfate, 10mM UDP-Glucose, 10 mM MgCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 54678 / Num. obs: 54022 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rsym value: 0.106
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Num. unique all: 5102 / Rsym value: 0.368 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.005data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JUJ

3juj


Resolution: 2.3→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2319 4.2 %RANDOM
Rwork0.23 43116 --
obs-45435 82 %-
Solvent computationBsol: 87.582 Å2
Displacement parametersBiso max: 73 Å2 / Biso mean: 25.749 Å2 / Biso min: 4.72 Å2
Baniso -1Baniso -2Baniso -3
1--7.137 Å20 Å2-2.984 Å2
2--2.651 Å20 Å2
3---4.485 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8394 0 156 736 9286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.557
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
X-RAY DIFFRACTION4UPG1.param

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