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- PDB-6hdm: R49A variant of beta-phosphoglucomutase from Lactococcus lactis c... -

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Basic information

Entry
Database: PDB / ID: 6hdm
TitleR49A variant of beta-phosphoglucomutase from Lactococcus lactis complexed with magnesium trifluoride and beta-G6P to 1.3 A.
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / metal fluoride / transition state analog
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
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 / Resolution: 1.3 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 17, 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)24,7428
Polymers24,1531
Non-polymers5897
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Homology to previously deposited structure (PDB 2WF5). Complex corroborated by NMR spectroscopy.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-5 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.300, 54.340, 104.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 24153.479 Da / Num. of mol.: 1 / Mutation: K125R, Y206H, R49A
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
#5: 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, 213 molecules

#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 24-34% PEG 4000 200mM sodium acetate 50mM TRIS pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.3→54.34 Å / Num. obs: 53048 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 21.1
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.263 / Num. unique obs: 2526 / CC1/2: 0.944 / Rpim(I) all: 0.138 / Rrim(I) all: 0.299 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WF5

2wf5


Resolution: 1.3→48.27 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.114 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14818 2686 5.1 %RANDOM
Rwork0.126 ---
obs0.12712 50290 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.053 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-0 Å20 Å2
2---0.31 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.3→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 35 207 1925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0141871
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171744
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6612537
X-RAY DIFFRACTIONr_angle_other_deg1.0571.6634094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5685238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6724.28691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9215328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.454158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022100
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02324
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_it1.4021.308934
X-RAY DIFFRACTIONr_mcbond_other1.4031.305933
X-RAY DIFFRACTIONr_mcangle_it1.9351.9741178
X-RAY DIFFRACTIONr_mcangle_other1.9351.9771179
X-RAY DIFFRACTIONr_scbond_it1.791.564937
X-RAY DIFFRACTIONr_scbond_other1.791.564937
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1432.2481360
X-RAY DIFFRACTIONr_long_range_B_refined2.816.1732062
X-RAY DIFFRACTIONr_long_range_B_other2.816.1862063
X-RAY DIFFRACTIONr_rigid_bond_restr1.39533615
X-RAY DIFFRACTIONr_sphericity_free18.8255146
X-RAY DIFFRACTIONr_sphericity_bonded12.08553648
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 176 -
Rwork0.143 3557 -
obs--96.26 %

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