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- PDB-5nzh: Crystal structure of UDP-glucose pyrophosphorylase V402W mutant f... -

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Basic information

Entry
Database: PDB / ID: 5nzh
TitleCrystal structure of UDP-glucose pyrophosphorylase V402W mutant from Leishmania major
ComponentsUDP-glucose pyrophosphorylase
KeywordsTRANSFERASE / NTP-transferase / Pathogen / Allostery / Catalysis
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / ciliary plasm / nuclear lumen / glycogen metabolic process / cytoplasm / cytosol
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex ...UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCramer, J.T. / Fuehring, J.I. / Baruch, P. / Bruetting, C. / Hesse, R. / Knoelker, H.-J. / Gerardy-Schahn, R. / Fedorov, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGZ: FE 1510/2-1 Germany
CitationJournal: Acs Catalysis / Year: 2018
Title: Decoding Allosteric Networks in Biocatalysts: Rational Approach to Therapies and Biotechnologies
Authors: Cramer, J.T. / Fuehring, J.I. / Baruch, P. / Bruetting, C. / Knoelker, H.-J. / Gerardy-Schahn, R. / Fedorov, R.
History
DepositionMay 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucose pyrophosphorylase
B: UDP-glucose pyrophosphorylase


Theoretical massNumber of molelcules
Total (without water)112,2842
Polymers112,2842
Non-polymers00
Water6,395355
1
A: UDP-glucose pyrophosphorylase


Theoretical massNumber of molelcules
Total (without water)56,1421
Polymers56,1421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-glucose pyrophosphorylase


Theoretical massNumber of molelcules
Total (without water)56,1421
Polymers56,1421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.560, 70.890, 112.290
Angle α, β, γ (deg.)90.00, 123.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

21A-760-

HOH

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Components

#1: Protein UDP-glucose pyrophosphorylase


Mass: 56141.852 Da / Num. of mol.: 2 / Mutation: V402W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: UGP, LMJF_18_0990 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4QDU3, UTP-glucose-1-phosphate uridylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 53.63 % / Mosaicity: 0.32 °
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 2.25M ammonium sulfate, 100mM Tris-HCl pH 7.2, 0.1% Tween 80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.9→47.854 Å / Num. obs: 26339 / % possible obs: 99.9 % / Redundancy: 7.04 % / Biso Wilson estimate: 21.83 Å2 / Rsym value: 0.0183 / Net I/σ(I): 4.37
Reflection shellMean I/σ(I) obs: 2.14 / Rsym value: 0.46

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SADABSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OEF

2oef


Resolution: 2.9→47.854 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.58
RfactorNum. reflection% reflection
Rfree0.2694 1396 5.31 %
Rwork0.2256 --
obs0.228 26290 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→47.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7465 0 0 355 7820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077610
X-RAY DIFFRACTIONf_angle_d0.87610311
X-RAY DIFFRACTIONf_dihedral_angle_d20.6112818
X-RAY DIFFRACTIONf_chiral_restr0.0621173
X-RAY DIFFRACTIONf_plane_restr0.0061335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.00370.36031350.29852462X-RAY DIFFRACTION100
3.0037-3.1240.36531450.2762484X-RAY DIFFRACTION100
3.124-3.26610.29891360.25382449X-RAY DIFFRACTION100
3.2661-3.43830.30141350.24212497X-RAY DIFFRACTION100
3.4383-3.65360.27781210.23512460X-RAY DIFFRACTION99
3.6536-3.93560.25921460.20592489X-RAY DIFFRACTION100
3.9356-4.33140.251520.19412485X-RAY DIFFRACTION100
4.3314-4.95760.21091250.18672492X-RAY DIFFRACTION100
4.9576-6.24390.24841460.24142500X-RAY DIFFRACTION100
6.2439-47.86050.26371550.2182576X-RAY DIFFRACTION100

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