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- PDB-5nzm: Crystal structure of UDP-glucose pyrophosphorylase from Leishmani... -

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Basic information

Entry
Database: PDB / ID: 5nzm
TitleCrystal structure of UDP-glucose pyrophosphorylase from Leishmania major in complex with murrayamine-I
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 / cytosol / cytoplasm
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
Murrayamine-I / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 1.1Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucose pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3922
Polymers56,0551
Non-polymers3371
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.110, 95.110, 72.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein UDP-glucose pyrophosphorylase


Mass: 56054.770 Da / Num. of mol.: 1
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: Chemical ChemComp-9ET / Murrayamine-I


Mass: 337.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.93 Å3/Da / Density % sol: 58.05 % / Mosaicity: 0.16 °
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 2.25 M ammonium sulfate, 100 mM Tris-HCl pH 7.2, 0.1% Tween 80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 27167 / % possible obs: 100 % / Redundancy: 12.17 % / Biso Wilson estimate: 38.5 Å2 / Rsym value: 0.035 / Net I/σ(I): 15.98
Reflection shellResolution: 2.35→2.45 Å / Mean I/σ(I) obs: 2.38 / Num. unique obs: 3182 / Rsym value: 0.401 / % possible all: 99.9

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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: 2.35→49.359 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.22
RfactorNum. reflection% reflection
Rfree0.2236 1315 4.84 %
Rwork0.2012 --
obs0.2021 27142 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→49.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 25 14 3769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033828
X-RAY DIFFRACTIONf_angle_d0.6635190
X-RAY DIFFRACTIONf_dihedral_angle_d15.3872319
X-RAY DIFFRACTIONf_chiral_restr0.043589
X-RAY DIFFRACTIONf_plane_restr0.004669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3502-2.44430.38281300.35082888X-RAY DIFFRACTION100
2.4443-2.55550.30561870.30312784X-RAY DIFFRACTION100
2.5555-2.69030.28851530.282848X-RAY DIFFRACTION100
2.6903-2.85880.32441740.26432827X-RAY DIFFRACTION100
2.8588-3.07950.30011260.25572887X-RAY DIFFRACTION100
3.0795-3.38930.27751480.23932850X-RAY DIFFRACTION100
3.3893-3.87960.22551190.21382898X-RAY DIFFRACTION100
3.8796-4.88720.19631360.15882888X-RAY DIFFRACTION100
4.8872-49.370.16351420.16472957X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 28.2494 Å / Origin y: 18.8266 Å / Origin z: -7.3975 Å
111213212223313233
T0.5072 Å2-0.0237 Å20.0293 Å2-0.4714 Å20.0043 Å2--0.4643 Å2
L1.1056 °2-0.815 °2-0.1537 °2-1.2462 °2-0.3654 °2--0.3361 °2
S0.0002 Å °0.0218 Å °-0.1276 Å °0.0462 Å °-0.014 Å °0.1192 Å °-0.0851 Å °0.0496 Å °0.001 Å °
Refinement TLS groupSelection details: all

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