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- PDB-6ydj: P146A variant of beta-phosphoglucomutase from Lactococcus lactis ... -

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Basic information

Entry
Database: PDB / ID: 6ydj
TitleP146A variant of beta-phosphoglucomutase from Lactococcus lactis in complex with glucose 6-phosphate and trifluoromagnesate
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / transition-state analogue / cis-trans proline isomerization / allomorphy / phosphoryl transfer
Function / homology
Function and homology information


beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
6-O-phosphono-beta-D-glucopyranose / TRIFLUOROMAGNESATE / 1,3-PROPANDIOL / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.04 Å
AuthorsWood, H.P. / Cruz-Navarrete, F.A. / Baxter, N.J. / Trevitt, C.R. / Robertson, A.J. / Dix, S.R. / Hounslow, A.M. / Cliff, M.J. / Waltho, J.P.
Funding support United Kingdom, Mexico, 6items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)X/009906-20-26 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M021637/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007965/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P007066/1 United Kingdom
Consejo Nacional de Ciencia y Tecnologia (CONACYT)472448 Mexico
Royal SocietyR/152968 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Allomorphy as a mechanism of post-translational control of enzyme activity.
Authors: Wood, H.P. / Cruz-Navarrete, F.A. / Baxter, N.J. / Trevitt, C.R. / Robertson, A.J. / Dix, S.R. / Hounslow, A.M. / Cliff, M.J. / Waltho, J.P.
History
DepositionMar 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7407
Polymers24,2141
Non-polymers5276
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-3 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.080, 54.250, 104.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Beta-phosphoglucomutase / Beta-PGM


Mass: 24213.557 Da / Num. of mol.: 1 / Mutation: P146A, K125R, Y206H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain IL1403) (lactic acid bacteria)
Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase
#2: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 214 molecules

#3: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F3Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.3 % / Description: Large plates
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000 (32% w/v), sodium acetate (200 mM), TRIS (100 mM), HEPES (13 mM), magnesium chloride (5 mM), EDTA (200 uM), sodium azide (500 uM), sodium fluoride (15 mM), glucose 6-phosphate (10 ...Details: PEG 4000 (32% w/v), sodium acetate (200 mM), TRIS (100 mM), HEPES (13 mM), magnesium chloride (5 mM), EDTA (200 uM), sodium azide (500 uM), sodium fluoride (15 mM), glucose 6-phosphate (10 mM), beta-phosphoglucomutase (0.4 mM)
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.04→54.25 Å / Num. obs: 101730 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 7.445 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.04-1.064.41.1381.150210.5440.6091.29599.3
2.82-54.326.946.5546210.0140.036100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.14 Å52.16 Å
Translation6.14 Å52.16 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
xia2data scaling
PHASER2.6.1phasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WF5

2wf5


Resolution: 1.04→52.21 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.753 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1685 5041 5 %RANDOM
Rwork0.1497 ---
obs0.1506 96597 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.64 Å2 / Biso mean: 12.63 Å2 / Biso min: 5.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 1.04→52.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 31 209 1918
Biso mean--10.45 24.02 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191765
X-RAY DIFFRACTIONr_bond_other_d0.0030.021697
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9922396
X-RAY DIFFRACTIONr_angle_other_deg0.90833954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.255229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79125.65876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44915311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.108157
X-RAY DIFFRACTIONr_chiral_restr0.0740.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211946
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02325
X-RAY DIFFRACTIONr_rigid_bond_restr2.05733462
X-RAY DIFFRACTIONr_sphericity_free22.6355139
X-RAY DIFFRACTIONr_sphericity_bonded6.59753502
LS refinement shellResolution: 1.04→1.067 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 390 -
Rwork0.317 6992 -
all-7382 -
obs--99.23 %

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