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- PDB-6h8y: T16A variant of beta-phosphoglucomutase from Lactococcus lactis i... -

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Basic information

Entry
Database: PDB / ID: 6h8y
TitleT16A variant of beta-phosphoglucomutase from Lactococcus lactis in an open conformer complexed with aluminium tetrafluoride to 1.9 A.
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / aluminium tetrafluoride / metal fluoride / transition state analogue
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 / : / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / : / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsRobertson, A.J. / Bisson, C. / Waltho, J.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M021637/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/K016245/1 United Kingdom
CitationJournal: To Be Published
Title: Transition state of phospho-enzyme hydrolysis in beta-phosphoglucomutase.
Authors: Robertson, A.J. / Bisson, C. / Waltho, J.P.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3373
Polymers24,2101
Non-polymers1272
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Structural homology to previously deposited PDBs; 2WFA, 2WF6. Furthermore, 19F Nuclear Magnetic Resonance spectroscopy was performed on the wild type variant, and the aluminium ...Evidence: homology, Structural homology to previously deposited PDBs; 2WFA, 2WF6. Furthermore, 19F Nuclear Magnetic Resonance spectroscopy was performed on the wild type variant, and the aluminium tetrafluoride species was confirmed to be in the active site.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-7 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.550, 52.840, 78.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-phosphoglucomutase / Beta-PGM


Mass: 24209.568 Da / Num. of mol.: 1 / Mutation: K125R, Y206H, T16A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (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
#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Crystallized in: 24-34% PEG 4000, 200 mM sodium acetate, 50 mM TRIS at pH 7.5
PH range: 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.89→31.46 Å / Num. obs: 18067 / % possible obs: 100 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.034 / Rrim(I) all: 0.102 / Net I/σ(I): 12.6
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.698 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 877 / CC1/2: 0.58 / Rpim(I) all: 0.593 / Rrim(I) all: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
Coot0.8.7model building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WHE

2whe


Resolution: 1.89→31.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.282 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25948 870 4.8 %RANDOM
Rwork0.20671 ---
obs0.20918 17149 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.914 Å2
Baniso -1Baniso -2Baniso -3
1-3.52 Å20 Å2-0 Å2
2---2.47 Å20 Å2
3----1.04 Å2
Refinement stepCycle: 1 / Resolution: 1.89→31.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 6 43 1727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191721
X-RAY DIFFRACTIONr_bond_other_d0.0020.021637
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9762331
X-RAY DIFFRACTIONr_angle_other_deg0.93933808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5865219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.13825.71477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.162157
X-RAY DIFFRACTIONr_chiral_restr0.0870.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211919
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02320
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6313.873876
X-RAY DIFFRACTIONr_mcbond_other2.6153.871875
X-RAY DIFFRACTIONr_mcangle_it3.4825.7951095
X-RAY DIFFRACTIONr_mcangle_other3.4815.7971096
X-RAY DIFFRACTIONr_scbond_it3.6074.348845
X-RAY DIFFRACTIONr_scbond_other3.6074.345839
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3956.321230
X-RAY DIFFRACTIONr_long_range_B_refined6.33547.2181948
X-RAY DIFFRACTIONr_long_range_B_other6.34547.1511938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 53 -
Rwork0.344 1252 -
obs--99.85 %

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