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- PDB-6hdg: D170N variant of beta-phosphoglucomutase from Lactococcus lactis ... -

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Basic information

Entry
Database: PDB / ID: 6hdg
TitleD170N variant of beta-phosphoglucomutase from Lactococcus lactis complexed with beta-G1P in a closed conformer to 1.2 A.
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase
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
1-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: 1.15 Å
AuthorsWood, H.P. / Robertson, 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)24,7707
Polymers24,2391
Non-polymers5316
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, homology to previously deposited structures with beta-G1P ligand.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint5 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.560, 55.080, 105.840
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: 24238.607 Da / Num. of mol.: 1 / Mutation: K125R, Y206H, D170N
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: Sugar ChemComp-XGP / 1-O-phosphono-beta-D-glucopyranose / 1-O-phosphono-beta-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
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: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.15→48.86 Å / Num. obs: 78880 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.037 / Rrim(I) all: 0.132 / Net I/σ(I): 10.8
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.986 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3894 / CC1/2: 0.562 / Rpim(I) all: 0.634 / Rrim(I) all: 2.087 / % possible all: 100

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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: 1.15→48.86 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.416 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17623 3872 4.9 %RANDOM
Rwork0.15033 ---
obs0.1516 74925 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.394 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å20 Å2
2---0.5 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.15→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 33 240 1962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0141854
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171763
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.6752510
X-RAY DIFFRACTIONr_angle_other_deg1.0011.6734145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.245237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32724.13887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92315337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.941158
X-RAY DIFFRACTIONr_chiral_restr0.070.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022032
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02312
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_it1.1011.223913
X-RAY DIFFRACTIONr_mcbond_other1.061.221912
X-RAY DIFFRACTIONr_mcangle_it1.3781.8461145
X-RAY DIFFRACTIONr_mcangle_other1.3921.8481146
X-RAY DIFFRACTIONr_scbond_it1.7441.479941
X-RAY DIFFRACTIONr_scbond_other1.7431.479941
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0432.1141360
X-RAY DIFFRACTIONr_long_range_B_refined2.17214.9271932
X-RAY DIFFRACTIONr_long_range_B_other1.97214.4741893
X-RAY DIFFRACTIONr_rigid_bond_restr1.59533617
X-RAY DIFFRACTIONr_sphericity_free15.95180
X-RAY DIFFRACTIONr_sphericity_bonded7.30853644
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 263 -
Rwork0.276 5476 -
obs--99.86 %

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