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- PDB-8q1d: D10N variant of beta-phosphoglucomutase from Lactococcus lactis i... -

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Basic information

Entry
Database: PDB / ID: 8q1d
TitleD10N variant of beta-phosphoglucomutase from Lactococcus lactis in complex with fructose 1,6-bisphosphate
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / mutase / complex
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 / 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: 1.75 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)24,7896
Polymers24,2391
Non-polymers5515
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-11 kcal/mol
Surface area10890 Å2
Unit cell
Length a, b, c (Å)31.888, 71.382, 83.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-phosphoglucomutase / Beta-PGM


Mass: 24238.609 Da / Num. of mol.: 1 / Mutation: D10N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
Gene: pgmB, LL0429, L0001 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase
#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.: 1 / 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 1.97 Å3/Da / Density % sol: 37.68 % / Description: needles
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.6 mM bPGM-D10N 5 mM MgCl2 50 mM fructose 1,6-bisphosphate 38 % PEG 4000 200 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: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→54.429 Å / Num. obs: 20093 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 18.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.043 / Net I/σ(I): 10.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 13 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1013 / CC1/2: 0.829 / Rpim(I) all: 0.379 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→54.429 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.137 / SU B: 3.844 / SU ML: 0.116 / Average fsc free: 0.9451 / Average fsc work: 0.964 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.143
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.252 965 4.815 %
Rwork0.161 19075 -
all0.165 --
obs-20040 99.915 %
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: 28.344 Å2
Baniso -1Baniso -2Baniso -3
1--2.477 Å2-0 Å20 Å2
2--3.688 Å2-0 Å2
3----1.211 Å2
Refinement stepCycle: LAST / Resolution: 1.75→54.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 33 188 1929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121780
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161729
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.6392410
X-RAY DIFFRACTIONr_angle_other_deg0.5121.5754001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.33157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53910314
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.231079
X-RAY DIFFRACTIONr_chiral_restr0.0790.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
X-RAY DIFFRACTIONr_nbd_refined0.2220.2365
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21592
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2874
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2919
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2860.222
X-RAY DIFFRACTIONr_nbd_other0.270.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2440.219
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
1.75-1.7960.262670.29313940.29214700.8970.90299.38780.292
1.796-1.8450.295690.26313330.26514020.9220.9211000.255
1.845-1.8980.265830.25412970.25413800.9350.9231000.241
1.898-1.9560.294640.22512890.22813530.920.9431000.205
1.956-2.020.259660.20912250.21112910.9390.9541000.187
2.02-2.0910.26600.17112040.17412640.9430.9731000.147
2.091-2.170.26510.16111680.16512190.9430.9761000.137
2.17-2.2590.223630.15111010.15511640.9650.9811000.127
2.259-2.3590.246410.13310910.13711320.9650.9861000.112
2.359-2.4740.275430.14810510.15310940.9580.9831000.125
2.474-2.6070.245560.1569730.16110300.9450.98299.90290.132
2.607-2.7650.269510.1479280.1539790.9530.9841000.122
2.765-2.9550.205470.1518730.1549200.9730.9841000.128
2.955-3.1910.28350.1588470.1628820.9460.9841000.137
3.191-3.4950.248400.1457470.157870.9680.9871000.131
3.495-3.9050.205410.1286980.1327390.9780.9911000.116
3.905-4.5060.222290.1186230.1226520.9730.9911000.108
4.506-5.5090.263250.1465370.1515620.9480.9871000.133
5.509-7.7510.443160.1824340.1894500.9280.981000.159
7.751-54.4290.242180.1522620.1582810.9790.98499.64410.154

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