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- PDB-8q1f: D10N,P146A variant of beta-phosphoglucomutase from Lactococcus la... -

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Basic information

Entry
Database: PDB / ID: 8q1f
TitleD10N,P146A variant of beta-phosphoglucomutase from Lactococcus lactis in complex with native beta-glucose 1,6-bisphosphate intermediate
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-glucopyranose / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 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

Downloads & links

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Assembly

Deposited unit
A: Beta-phosphoglucomutase
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,58315
Polymers48,4252
Non-polymers1,15713
Water8,737485
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-37 kcal/mol
Surface area19900 Å2
Unit cell
Length a, b, c (Å)32.023, 79.663, 79.848
Angle α, β, γ (deg.)90.000, 97.614, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Beta-phosphoglucomutase


Mass: 24212.572 Da / Num. of mol.: 2 / 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-B16 / 1,6-di-O-phosphono-beta-D-glucopyranose / 1,6-di-O-phosphono-beta-D-glucose / 1,6-di-O-phosphono-D-glucose / 1,6-di-O-phosphono-glucose


Type: D-saccharide / Mass: 340.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Glcp1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 496 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.09 Å3/Da / Density % sol: 41.11 % / Description: needles
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.6 mM bPGM-D10N,P146A 50 mM MgCl2 10 mM bG16BP 28% 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: I03 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.01→39.83 Å / Num. obs: 166355 / % possible obs: 80.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 7.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.016 / Net I/σ(I): 26
Reflection shellResolution: 1.01→1.03 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1151 / CC1/2: 0.743 / Rpim(I) all: 0.386

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.01→39.83 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.698 / SU ML: 0.016 / Cross valid method: FREE R-VALUE / ESU R: 0.023 / ESU R Free: 0.024
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1348 8222 4.944 %
Rwork0.1152 158091 -
all0.116 --
obs-166313 80.296 %
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: 14.316 Å2
Baniso -1Baniso -2Baniso -3
1--0.047 Å20 Å20.046 Å2
2--0.618 Å2-0 Å2
3----0.564 Å2
Refinement stepCycle: LAST / Resolution: 1.01→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 67 485 3964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123668
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163618
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.6374985
X-RAY DIFFRACTIONr_angle_other_deg0.5191.5768392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5255480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.599515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20910673
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.98410160
X-RAY DIFFRACTIONr_chiral_restr0.0750.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024205
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02755
X-RAY DIFFRACTIONr_nbd_refined0.2350.2727
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.23196
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21812
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21851
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2285
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.216
X-RAY DIFFRACTIONr_nbd_other0.1980.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.245
X-RAY DIFFRACTIONr_rigid_bond_restr28.83537286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.0360.295990.2782035X-RAY DIFFRACTION13.9241
1.036-1.0650.2382010.2254309X-RAY DIFFRACTION30.3479
1.065-1.0960.1943350.1846532X-RAY DIFFRACTION47.5455
1.096-1.1290.1655060.1498502X-RAY DIFFRACTION64.2007
1.129-1.1660.1435440.12410788X-RAY DIFFRACTION83.0792
1.166-1.2070.1246460.10611925X-RAY DIFFRACTION95.1556
1.207-1.2530.1255500.10511743X-RAY DIFFRACTION96.8487
1.253-1.3040.136040.10311327X-RAY DIFFRACTION97.2847
1.304-1.3620.1325900.09910931X-RAY DIFFRACTION97.7599
1.362-1.4280.1275520.09210490X-RAY DIFFRACTION98.1424
1.428-1.5050.1135230.08710028X-RAY DIFFRACTION98.497
1.505-1.5960.1155230.0819485X-RAY DIFFRACTION98.708
1.596-1.7060.1124790.0848935X-RAY DIFFRACTION99.1052
1.706-1.8430.134090.0938383X-RAY DIFFRACTION99.5133
1.843-2.0180.1233950.1017738X-RAY DIFFRACTION99.6203
2.018-2.2560.1293760.1067029X-RAY DIFFRACTION99.919
2.256-2.6030.1413210.1246205X-RAY DIFFRACTION100
2.603-3.1850.1472560.1365306X-RAY DIFFRACTION100
3.185-4.490.142100.1274072X-RAY DIFFRACTION100
4.49-39.830.1591030.1712326X-RAY DIFFRACTION100

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