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- PDB-8q1c: Substrate-free D10N,P146A variant of beta-phosphoglucomutase from... -

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Basic information

Entry
Database: PDB / ID: 8q1c
TitleSubstrate-free D10N,P146A variant of beta-phosphoglucomutase from Lactococcus lactis
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
PHOSPHATE ION / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.679 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)48,9709
Polymers48,4252
Non-polymers5457
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-22 kcal/mol
Surface area20990 Å2
Unit cell
Length a, b, c (Å)38.650, 117.251, 53.250
Angle α, β, γ (deg.)90.000, 98.637, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 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

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Non-polymers , 5 types, 192 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.47 Å3/Da / Density % sol: 50.16 % / Description: rods
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.6 mM bPGM-D10N,P146A 5 mM MgCl2 3 mM AlCl3 20 mM NaF 15 mM glucose 6-phosphate 32 % PEG 4000 200 mM sodium acetate 200 mM tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.679→117.25 Å / Num. obs: 52374 / % possible obs: 98.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.04 / Net I/σ(I): 13.8
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2284 / CC1/2: 0.277 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.679→52.702 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.26 / WRfactor Rwork: 0.201 / SU B: 4.146 / SU ML: 0.127 / Average fsc free: 0.9315 / Average fsc work: 0.951 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2702 2655 5.073 %
Rwork0.2108 49681 -
all0.214 --
obs-52336 98.202 %
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: 39.612 Å2
Baniso -1Baniso -2Baniso -3
1-2.135 Å20 Å20.763 Å2
2---1.294 Å20 Å2
3----1.025 Å2
Refinement stepCycle: LAST / Resolution: 1.679→52.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 32 185 3591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123457
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163379
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.6294674
X-RAY DIFFRACTIONr_angle_other_deg0.5481.5767799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1495436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.781514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47110610
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.9310152
X-RAY DIFFRACTIONr_chiral_restr0.0840.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023970
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
X-RAY DIFFRACTIONr_nbd_refined0.2320.2685
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.23018
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21730
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21834
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2156
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1410.27
X-RAY DIFFRACTIONr_nbd_other0.1510.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0950.210
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
1.679-1.7230.3711800.37633050.37539120.8730.88189.08490.375
1.723-1.770.3641960.35834940.35838500.8780.88695.84420.357
1.77-1.8210.3621810.32734720.32937070.9070.9198.54330.323
1.821-1.8770.3131950.2833460.28235890.9270.93698.66260.27
1.877-1.9390.3371720.26433160.26835410.9170.94798.50330.243
1.939-2.0070.3121650.2631730.26233850.930.95398.61150.238
2.007-2.0830.3011600.23630700.23932690.930.96198.8070.211
2.083-2.1670.3031730.22729770.23231850.940.96698.90110.2
2.167-2.2640.3031350.21228580.21730190.9410.9799.13880.189
2.264-2.3740.3031430.20227030.20728660.9490.97499.30220.177
2.374-2.5020.2731390.20226010.20527550.9530.97599.45550.178
2.502-2.6530.2621320.19324740.19726180.9590.97799.54160.173
2.653-2.8360.2711150.19723090.224360.9490.97799.50740.179
2.836-3.0630.2891090.22621810.22922940.9470.96899.82560.213
3.063-3.3540.2641070.21719970.21921090.9480.97299.76290.21
3.354-3.7480.294990.22317980.22718980.9440.97699.94730.224
3.748-4.3240.2011040.17215860.17316900.9770.9841000.18
4.324-5.2870.193630.15713590.15814220.9760.9861000.174
5.287-7.4390.276510.18910640.19311150.9690.9851000.205
7.439-52.7020.256360.1735990.1796350.9620.9811000.203

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