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- PDB-7ppr: The structure of UDP-glucose pyrophosphorylase from Aspergillus f... -

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Basic information

Entry
Database: PDB / ID: 7ppr
TitleThe structure of UDP-glucose pyrophosphorylase from Aspergillus fumigatus
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / UGP / UDP-glucose pyrophosphorylase
Function / homologyUTP--glucose-1-phosphate uridylyltransferase / sporulation / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / Nucleotide-diphospho-sugar transferases / UTP--glucose-1-phosphate uridylyltransferase
Function and homology information
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsMorton, S. / Raimi, O.G. / Yan, K. / van Aalten, D.M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)V001094 United Kingdom
CitationJournal: To Be Published
Title: Genetic and structural validation of UDP-glucose pyrophosphorylase as a novel antifungal target against Aspergillus fumigatus
Authors: Yan, K. / Raimi, O.G. / Morton, S. / Ferenbach, A.T. / Wei, P. / Yuan, H. / Fang, W. / van Aalten, D.M.F.
History
DepositionSep 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,26519
Polymers109,7532
Non-polymers1,51217
Water2,360131
1
A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules

A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules

A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules

A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)445,05976
Polymers439,0128
Non-polymers6,04768
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area26750 Å2
ΔGint-886 kcal/mol
Surface area165040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.160, 152.610, 160.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 32 - 511 / Label seq-ID: 13 - 492

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein UTP--glucose-1-phosphate uridylyltransferase


Mass: 54876.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: E9R9Z5, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.99 Å3/Da / Density % sol: 69.18 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.8 M lithium sulphate monohydrate, and 0.1 M sodium acetate trihydrate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9281 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9281 Å / Relative weight: 1
ReflectionResolution: 2.57→80.01 Å / Num. obs: 52428 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.99 / Net I/σ(I): 15.2
Reflection shellResolution: 2.57→2.65 Å / Num. unique obs: 4513 / CC1/2: 0.514

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I5K

2i5k


Resolution: 2.57→80 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.671 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.348 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 2699 5.1 %RANDOM
Rwork0.227 ---
obs0.2295 49727 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 196.83 Å2 / Biso mean: 68.311 Å2 / Biso min: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20 Å2
2---0.03 Å20 Å2
3---1.18 Å2
Refinement stepCycle: final / Resolution: 2.57→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6903 0 77 131 7111
Biso mean--116.67 60.56 -
Num. residues----914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137167
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176593
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.6369748
X-RAY DIFFRACTIONr_angle_other_deg1.2041.57515234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0315921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55822.738347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.284151162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5121542
X-RAY DIFFRACTIONr_chiral_restr0.0730.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028041
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021425
Refine LS restraints NCS

Ens-ID: 1 / Number: 11649 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.57→2.637 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 186 -
Rwork0.372 3682 -
all-3868 -
obs--99.87 %

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