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- PDB-8q1e: D10N,P146A variant of beta-phosphoglucomutase from Lactococcus la... -

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Basic information

Entry
Database: PDB / ID: 8q1e
TitleD10N,P146A variant of beta-phosphoglucomutase from Lactococcus lactis in complex with fructose 1,6-bisphosphate
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / mutase
Function / homology
Function and homology information


beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function
Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / : / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsCruz-Navarrete, F.A. / Baxter, N.J. / Flinders, A.J. / Buzoianu, A. / Cliff, M.J. / Baker, P.J. / Waltho, J.P.
Funding support Mexico, United Kingdom, 3items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)472448 Mexico
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M021637/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007965/1 United Kingdom
CitationJournal: Commun Biol / Year: 2024
Title: Peri active site catalysis of proline isomerisation is the molecular basis of allomorphy in beta-phosphoglucomutase.
Authors: Cruz-Navarrete, F.A. / Baxter, N.J. / Flinders, A.J. / Buzoianu, A. / Cliff, M.J. / Baker, P.J. / Waltho, J.P.
History
DepositionJul 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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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)24,6886
Polymers24,2131
Non-polymers4755
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-30 kcal/mol
Surface area10850 Å2
Unit cell
Length a, b, c (Å)32.120, 83.757, 38.890
Angle α, β, γ (deg.)90.000, 110.661, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-phosphoglucomutase


Mass: 24212.572 Da / Num. of mol.: 1 / Mutation: D10N and P146A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
Gene: JCM5805K_2499 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A7T4I1
#2: Sugar ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.16 % / Description: needles
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.6 mM bPGM-D10N,P146A 50 mM MgCl2 50 mM F16BP 32 % PEG 4000 100 mM sodium acetate 100 mM tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9227 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9227 Å / Relative weight: 1
ReflectionResolution: 1.23→83.76 Å / Num. obs: 55719 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Net I/σ(I): 12.3
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2694 / CC1/2: 0.315 / Rpim(I) all: 0.953 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→41.913 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.856 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.046
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1942 2670 4.795 %
Rwork0.1516 53014 -
all0.154 --
obs-55684 99.898 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.565 Å2
Baniso -1Baniso -2Baniso -3
1--0.606 Å2-0 Å20.505 Å2
2--0.069 Å20 Å2
3---0.122 Å2
Refinement stepCycle: LAST / Resolution: 1.23→41.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 27 127 1860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0121771
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161723
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.6352400
X-RAY DIFFRACTIONr_angle_other_deg0.421.5743985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2715224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.8457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92210316
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.8271078
X-RAY DIFFRACTIONr_chiral_restr0.0580.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02365
X-RAY DIFFRACTIONr_nbd_refined0.2280.2345
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.21490
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2870
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.274
X-RAY DIFFRACTIONr_metal_ion_refined0.0280.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.28
X-RAY DIFFRACTIONr_nbd_other0.2260.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1010.27
X-RAY DIFFRACTIONr_rigid_bond_restr20.11233494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.23-1.2620.3631830.34238350.34340750.8950.90798.60120.35
1.262-1.2960.3441790.33338560.33340350.9020.9081000.34
1.296-1.3340.332290.32136690.32138980.9120.9131000.328
1.334-1.3750.3161770.30135860.30237630.9180.9291000.307
1.375-1.420.2651890.26934960.26936850.950.9451000.273
1.42-1.4690.2681510.24234060.24335570.9460.9551000.241
1.469-1.5250.2391680.19832580.234260.960.9721000.189
1.525-1.5870.2081520.16131240.16332760.9720.9821000.147
1.587-1.6570.1671220.13430320.13631540.9830.9881000.118
1.657-1.7380.2111340.12828940.13130280.9740.9891000.109
1.738-1.8320.1821580.11627280.1228860.9790.9921000.098
1.832-1.9430.2081300.11826250.12227550.9750.9911000.101
1.943-2.0770.2051330.11924050.12325380.9750.9921000.105
2.077-2.2430.1621150.12222760.12523910.9850.9921000.109
2.243-2.4560.1811030.12421000.12722030.9810.9911000.111
2.456-2.7450.21030.13818830.14219860.9760.9891000.126
2.745-3.1670.176780.13616850.13717630.980.9891000.128
3.167-3.8730.141720.11514310.11615030.9890.9921000.114
3.873-5.4550.142560.1211000.12111560.9920.9921000.127
5.455-41.9130.171380.1656250.1656630.9850.9841000.188

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