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

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Basic information

Entry
Database: PDB / ID: 6hdk
TitleR49A variant of beta-phosphoglucomutase from Lactococcus lactis complexed with aluminium tetrafluoride and beta-G6P to 1.2 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 / Phosphoglycolate phosphatase-like, domain 2 / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / 6-O-phosphono-beta-D-glucopyranose / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 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

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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)24,7739
Polymers24,1531
Non-polymers6208
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Homology to previously deposited structure (PDB 2WF6), complex corroborated by NMR spectroscopy.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-16 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.230, 54.290, 104.240
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) (unknown) / References: UniProt: P71447, beta-phosphoglucomutase
#6: 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 , 5 types, 216 molecules

#2: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
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 6M / Detector: PIXEL / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.24→54.29 Å / Num. obs: 60728 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.04 / Rrim(I) all: 0.107 / Net I/σ(I): 10.1
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.019 / Num. unique obs: 2904 / CC1/2: 0.53 / Rpim(I) all: 0.48 / Rrim(I) all: 1.131 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WF6
Resolution: 1.24→52.17 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.668 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.039 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16724 2983 4.9 %RANDOM
Rwork0.13593 ---
obs0.13746 57667 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.71 Å20 Å2
3---1.02 Å2
Refinement stepCycle: 1 / Resolution: 1.24→52.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 36 209 1928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0141769
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171668
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.6612396
X-RAY DIFFRACTIONr_angle_other_deg1.0671.6633910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.525226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31524.75682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78815311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.067156
X-RAY DIFFRACTIONr_chiral_restr0.0780.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02302
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_it1.6261.339886
X-RAY DIFFRACTIONr_mcbond_other1.6091.335885
X-RAY DIFFRACTIONr_mcangle_it2.1422.021109
X-RAY DIFFRACTIONr_mcangle_other2.1552.0231110
X-RAY DIFFRACTIONr_scbond_it2.4011.653883
X-RAY DIFFRACTIONr_scbond_other2.41.653883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8992.351285
X-RAY DIFFRACTIONr_long_range_B_refined3.50717.4512016
X-RAY DIFFRACTIONr_long_range_B_other3.50817.4512014
X-RAY DIFFRACTIONr_rigid_bond_restr1.78533437
X-RAY DIFFRACTIONr_sphericity_free23.335136
X-RAY DIFFRACTIONr_sphericity_bonded10.78253486
LS refinement shellResolution: 1.24→1.272 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 219 -
Rwork0.27 4125 -
obs--98.53 %

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