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- PDB-6ydk: Substrate-free P146A variant of beta-phosphoglucomutase from Lact... -

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Basic information

Entry
Database: PDB / ID: 6ydk
TitleSubstrate-free P146A variant of beta-phosphoglucomutase from Lactococcus lactis
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / cis-trans proline isomerization / allomorphy / phosphoryl transfer / enzyme regulation
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
Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 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)24,2382
Polymers24,2141
Non-polymers241
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.300, 56.240, 77.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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)
Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 9.62 Å3/Da / Density % sol: 87.21 % / Description: Thin rod shaped
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000 (24% w/v), sodium acetate (200 mM), TRIS (100 mM), HEPES (50 mM), magnesium chloride (5 mM), EDTA (1 mM), sodium azide (2 mM), beta-phosphoglucomutase (0.5 mM). Seeded with 10,000x ...Details: PEG 4000 (24% w/v), sodium acetate (200 mM), TRIS (100 mM), HEPES (50 mM), magnesium chloride (5 mM), EDTA (1 mM), sodium azide (2 mM), beta-phosphoglucomutase (0.5 mM). Seeded with 10,000x dilution of much smaller protein crystals grown under the same conditions but with 0.2 mM beta-phosphoglucomutase.
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 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2018
RadiationMonochromator: 0.9795 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.02→43.95 Å / Num. obs: 15683 / % possible obs: 98.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 32.196 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.031 / Rrim(I) all: 0.081 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.02-2.053.70.9531.26860.5560.5061.0988.9
5.48-43.966.441.989510.0120.032100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.31 Å43.95 Å
Translation6.31 Å43.95 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
xia2data scaling
PHASER2.6.1phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WHE

2whe


Resolution: 2.02→43.95 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.417 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.178
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 777 5 %RANDOM
Rwork0.2156 ---
obs0.2174 14863 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.67 Å2 / Biso mean: 42.707 Å2 / Biso min: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-0 Å2
2---0.36 Å20 Å2
3---0.63 Å2
Refinement stepCycle: final / Resolution: 2.02→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 1 34 1741
Biso mean--45.54 38.25 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191742
X-RAY DIFFRACTIONr_bond_other_d0.0020.021709
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9772357
X-RAY DIFFRACTIONr_angle_other_deg0.95833947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.88625.76978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02515313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.923157
X-RAY DIFFRACTIONr_chiral_restr0.080.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211978
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02363
LS refinement shellResolution: 2.02→2.072 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 60 -
Rwork0.317 960 -
all-1020 -
obs--88.7 %

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