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- PDB-6h8z: T16A variant of beta-phosphoglucomutase from Lactococcus lactis i... -

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Basic information

Entry
Database: PDB / ID: 6h8z
TitleT16A variant of beta-phosphoglucomutase from Lactococcus lactis in an open conformer complexed with magnesium trifluoride to 1.6 A.
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / magnesium trifluoride / 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
TRIFLUOROMAGNESATE / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)24,3774
Polymers24,2101
Non-polymers1683
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Homology to PDB: 2WFA and 2WF5 where BeF and MgF moieties localize to the active site. Furthermore, 19F Nuclear Magnetic Resonance spectroscopy was performed on the wild type ...Evidence: homology, Homology to PDB: 2WFA and 2WF5 where BeF and MgF moieties localize to the active site. Furthermore, 19F Nuclear Magnetic Resonance spectroscopy was performed on the wild type variant of this complex, and the MgFx moiety was confirmed to localize to the active site.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-4 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.267, 53.887, 82.269
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 (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
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 24-34% PEG4000, 200 mM sodium acetate, 50 mM TRIS 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: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→45.08 Å / Num. obs: 28426 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Rrim(I) all: 0.072 / Net I/σ(I): 10.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.715 / Num. unique obs: 1409 / CC1/2: 0.579 / Rpim(I) all: 0.703 / Rrim(I) all: 1.857 / % possible all: 99.4

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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: 1.6→45.08 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.72 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28368 1359 4.8 %RANDOM
Rwork0.23639 ---
obs0.23861 26851 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.527 Å2
Baniso -1Baniso -2Baniso -3
1-4.17 Å20 Å2-0 Å2
2---2.38 Å20 Å2
3----1.79 Å2
Refinement stepCycle: 1 / Resolution: 1.6→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 9 73 1769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191733
X-RAY DIFFRACTIONr_bond_other_d0.0020.021664
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9792341
X-RAY DIFFRACTIONr_angle_other_deg0.95433871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0235220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33725.65876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42315308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.714157
X-RAY DIFFRACTIONr_chiral_restr0.0810.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02321
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_it2.0413.174880
X-RAY DIFFRACTIONr_mcbond_other2.0433.171879
X-RAY DIFFRACTIONr_mcangle_it2.8864.7491100
X-RAY DIFFRACTIONr_mcangle_other2.8854.7531101
X-RAY DIFFRACTIONr_scbond_it2.6083.564853
X-RAY DIFFRACTIONr_scbond_other2.6043.564853
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9425.1871242
X-RAY DIFFRACTIONr_long_range_B_refined5.29638.4121919
X-RAY DIFFRACTIONr_long_range_B_other5.45338.3711902
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.519 87 -
Rwork0.457 1943 -
obs--98.64 %

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