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- PDB-5ok0: Structure of the D10N mutant of beta-phosphoglucomutase from Lact... -

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Basic information

Entry
Database: PDB / ID: 5ok0
TitleStructure of the D10N mutant of beta-phosphoglucomutase from Lactococcus lactis trapped with native reaction intermediate beta-glucose 1,6-bisphosphate to 2.2A resolution.
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / bisphospho-intermediate
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 / haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily ...Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-glucopyranose / 1,3-PROPANDIOL / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRobertson, A.J. / Bisson, C.
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: Acs Catalysis / Year: 2018
Title: van der Waals Contact between Nucleophile and Transferring Phosphorus Is Insufficient To Achieve Enzyme Transition-State Architecture
Authors: Johnson, L.A. / Robertson, A.J. / Baxter, N.J. / Trevitt, C.R. / Bisson, C. / Jin, Y. / Wood, H.P. / Hounslow, A.M. / Cliff, M.J. / Blackburn, G.M. / Bowler, M.W. / Waltho, J.P.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2934
Polymers23,8521
Non-polymers4413
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, homology to previously deposited structures 1ZOL, 1O03, 1O08, 1Z4N, 1Z4O, 1LVH, 2WF5, 2WF6, 2WF7, 2WF8, 2WF9, 2WFA, 2WHE, 3FM9, 3ZI4, 4C4R, 4C4S, 4C4T
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-6 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.810, 54.940, 103.340
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: 23852.119 Da / Num. of mol.: 1 / Mutation: K125R, Y206H, D10N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (unknown) / References: UniProt: P71447, beta-phosphoglucomutase
#2: Sugar ChemComp-B16 / 1,6-di-O-phosphono-beta-D-glucopyranose


Type: D-saccharide / Mass: 340.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Glcp1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PDO / 1,3-PROPANDIOL / 1,3-Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 43.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 24-34% PEG 4000 200mM Tris pH 7.5 200mM sodium acetate harvested after 1 week
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 PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→48.51 Å / Num. obs: 11990 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.98 / Rmerge(I) obs: 0.339 / Rpim(I) all: 0.148 / Net I/σ(I): 5.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.683 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 598 / CC1/2: 0.391 / Rpim(I) all: 0.721 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
Coot0.8.1model building
XDSdata reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WF5
Resolution: 2.15→48.51 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.889 / SU B: 11.097 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.254 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29234 571 4.8 %RANDOM
Rwork0.2201 ---
obs0.2235 11376 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.793 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å2-0 Å2-0 Å2
2---0.87 Å20 Å2
3---2.62 Å2
Refinement stepCycle: 1 / Resolution: 2.15→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 26 84 1790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191735
X-RAY DIFFRACTIONr_bond_other_d0.0020.021686
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9712348
X-RAY DIFFRACTIONr_angle_other_deg0.9972.993896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.34225.65876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8315301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.012157
X-RAY DIFFRACTIONr_chiral_restr0.080.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211933
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
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_it1.7743.057871
X-RAY DIFFRACTIONr_mcbond_other1.7393.055870
X-RAY DIFFRACTIONr_mcangle_it2.7814.5781087
X-RAY DIFFRACTIONr_mcangle_other2.7824.581088
X-RAY DIFFRACTIONr_scbond_it2.1863.305864
X-RAY DIFFRACTIONr_scbond_other2.1843.305864
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5464.8461262
X-RAY DIFFRACTIONr_long_range_B_refined4.90223.7891868
X-RAY DIFFRACTIONr_long_range_B_other4.90123.7941869
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 44 -
Rwork0.348 810 -
obs--99.88 %

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