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- PDB-7p5o: Crystal structure of Aspergillus fumigatus phosphoglucomutase in ... -

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Basic information

Entry
Database: PDB / ID: 7p5o
TitleCrystal structure of Aspergillus fumigatus phosphoglucomutase in complex with the reaction intermediate
ComponentsPhosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / sugar nucleotide / glucan / UDP-Glc
Function / homology
Function and homology information


phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function
Phosphoglucomutase / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. ...Phosphoglucomutase / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
Similarity search - Domain/homology
1,6-di-O-phosphono-alpha-D-glucopyranose / Phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.48 Å
AuthorsRaimi, 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: Targeting an essential step in the biosynthetic pathway of uridine diphosphate glucose in Aspergillus fumigatus
Authors: Yan, K. / Stanley, M. / Kowalski, B. / Raimi, O.G. / Ferenbach, A.T. / Wei, P.Z. / Yuan, H. / Fang, W. / van Aalten, D.M.F.
History
DepositionJul 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 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

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Assembly

Deposited unit
A: Phosphoglucomutase
B: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,6906
Polymers121,9632
Non-polymers7274
Water9,188510
1
A: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3453
Polymers60,9821
Non-polymers3632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3453
Polymers60,9821
Non-polymers3632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.570, 209.610, 61.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: -2 - 555 / Label seq-ID: 3 - 560

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

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Components

#1: Protein Phosphoglucomutase


Mass: 60981.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: CDV57_06471 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A229WAX6
#2: Sugar ChemComp-G16 / 1,6-di-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE / 1,6-di-O-phosphono-alpha-D-glucose / 1,6-di-O-phosphono-D-glucose / 1,6-di-O-phosphono-glucose


Type: D-saccharide / Mass: 339.108 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 90 mM sodium fluoride, 90 mM sodium bromide, 90 mM sodium iodide, 100 mM Tris-bicine pH 8.5, 20% v/v polyethylene glycol 550 MME, 10 % w/v polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.48→89.2 Å / Num. obs: 44960 / % possible obs: 98.4 % / Redundancy: 4.2 % / CC1/2: 0.994 / Net I/σ(I): 11.2
Reflection shellResolution: 2.48→2.53 Å / Num. unique obs: 2259 / CC1/2: 0.795

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EPC

5epc


Resolution: 2.48→89.2 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 12.188 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.616 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 2250 5 %RANDOM
Rwork0.2011 ---
obs0.2041 42710 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.27 Å2 / Biso mean: 37.597 Å2 / Biso min: 12.46 Å2
Baniso -1Baniso -2Baniso -3
1--2.75 Å20 Å20 Å2
2--0.24 Å20 Å2
3---2.51 Å2
Refinement stepCycle: final / Resolution: 2.48→89.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8545 0 42 510 9097
Biso mean--31.35 35.66 -
Num. residues----1114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138790
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178065
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.64511916
X-RAY DIFFRACTIONr_angle_other_deg1.2721.58318801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.52351117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69123.9400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.859151464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0331528
X-RAY DIFFRACTIONr_chiral_restr0.0940.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021762
Refine LS restraints NCS

Ens-ID: 1 / Number: 17529 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.484→2.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 158 -
Rwork0.424 3176 -
all-3334 -
obs--99.52 %

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