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- PDB-6h90: K145A variant of beta-phosphoglucomutase from Lactococcus lactis ... -

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Basic information

Entry
Database: PDB / ID: 6h90
TitleK145A variant of beta-phosphoglucomutase from Lactococcus lactis inhibited by beryllium trifluoride to 1.3 A.
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / beryllium trifluoride / phospho-enzyme analog / metal fluoride
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
BERYLLIUM TRIFLUORIDE ION / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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)24,5438
Polymers24,1811
Non-polymers3627
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Homology to previously deposited PDB: 2WFA. Furthermore, 1D fluorine NMR of the complex confirmed the presence of the beryllium trifluoride moiety.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-3 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.320, 53.630, 81.500
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 , 1 types, 1 molecules A

#1: Protein Beta-phosphoglucomutase / Beta-PGM


Mass: 24181.492 Da / Num. of mol.: 1 / Mutation: K145A
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

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Non-polymers , 5 types, 296 molecules

#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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 24-34% PEG 4000 200mM sodium acetate 100mM TRIS pH 7.5
PH range: 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.31→40.75 Å / Num. obs: 55835 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Net I/σ(I): 13.1
Reflection shellResolution: 1.31→1.34 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.101 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4062 / CC1/2: 0.539 / Rpim(I) all: 0.517 / Rrim(I) all: 1.335 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
Coot0.8.9.1model building
xia23diidata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WHE

2whe


Resolution: 1.31→40.75 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.684 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.043 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1627 2832 5.1 %RANDOM
Rwork0.13525 ---
obs0.13672 52935 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.262 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å2-0 Å20 Å2
2---0.38 Å2-0 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.31→40.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 22 289 1996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0141794
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171703
X-RAY DIFFRACTIONr_angle_refined_deg1.491.6482428
X-RAY DIFFRACTIONr_angle_other_deg1.081.6593993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3185234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91424.0786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31815322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.832158
X-RAY DIFFRACTIONr_chiral_restr0.2170.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022017
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02311
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_it1.3321.32903
X-RAY DIFFRACTIONr_mcbond_other1.3321.316902
X-RAY DIFFRACTIONr_mcangle_it1.7161.9921136
X-RAY DIFFRACTIONr_mcangle_other1.7151.9961137
X-RAY DIFFRACTIONr_scbond_it2.4261.699891
X-RAY DIFFRACTIONr_scbond_other2.4261.699891
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8942.41289
X-RAY DIFFRACTIONr_long_range_B_refined3.18818.1322130
X-RAY DIFFRACTIONr_long_range_B_other3.19118.1392131
X-RAY DIFFRACTIONr_rigid_bond_restr1.91533497
X-RAY DIFFRACTIONr_sphericity_free21.7855171
X-RAY DIFFRACTIONr_sphericity_bonded10.6653586
LS refinement shellResolution: 1.31→1.344 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 193 -
Rwork0.28 3865 -
obs--99.93 %

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