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- PDB-6h8x: Beta-phosphoglucomutase from Lactococcus lactis in an open confor... -

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Basic information

Entry
Database: PDB / ID: 6h8x
TitleBeta-phosphoglucomutase from Lactococcus lactis in an open conformer complexed with magnesium trifluoride to 1.8 A.
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / magnesium trifluoride / metal fluoride / transition state analogue
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 / : / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / : / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / TRIFLUOROMAGNESATE / 1,3-PROPANDIOL / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsRobertson, A.J. / Bisson, C. / Waltho, J.P.
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: To Be Published
Title: Transition state of phospho-enzyme hydrolysis in beta-phosphoglucomutase.
Authors: Robertson, A.J. / Bisson, C. / Waltho, J.P.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)49,32216
Polymers48,4792
Non-polymers84314
Water3,837213
1
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5907
Polymers24,2401
Non-polymers3516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7329
Polymers24,2401
Non-polymers4928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.160, 116.980, 53.110
Angle α, β, γ (deg.)90.00, 98.93, 90.00
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 / Beta-PGM


Mass: 24239.594 Da / Num. of mol.: 2 / Mutation: K125R, Y206H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain IL1403) (lactic acid bacteria)
Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase

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Non-polymers , 6 types, 227 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F3Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PDO / 1,3-PROPANDIOL


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


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Initial (open) crystals grown in: 24-32% PEG 4000 200 mM sodium acetate 50 mM TRIS pH 7.5 Crystals cryoprotected in original mother liquor plus: 25% ethylene glycol 15 mM sodium fluoride
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 PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.83→23.4 Å / Num. obs: 39841 / % possible obs: 98.5 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.04 / Rrim(I) all: 0.108 / Net I/σ(I): 11.6
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.258 / Num. unique obs: 1922 / CC1/2: 0.568 / Rpim(I) all: 0.501 / Rrim(I) all: 1.355 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
Coot0.8.7model building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WHE

2whe


Resolution: 1.83→23.31 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.6 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.131 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22583 1943 4.9 %RANDOM
Rwork0.18265 ---
obs0.18477 37867 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.521 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.67 Å2
2--0.28 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.83→23.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 51 213 3642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193484
X-RAY DIFFRACTIONr_bond_other_d0.0020.023348
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9814692
X-RAY DIFFRACTIONr_angle_other_deg0.91737783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.22325.686153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88315611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6421514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02640
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_it2.0072.9211756
X-RAY DIFFRACTIONr_mcbond_other22.9191754
X-RAY DIFFRACTIONr_mcangle_it2.8144.3722192
X-RAY DIFFRACTIONr_mcangle_other2.8134.3732193
X-RAY DIFFRACTIONr_scbond_it2.83.3521728
X-RAY DIFFRACTIONr_scbond_other2.7993.3531729
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4114.852501
X-RAY DIFFRACTIONr_long_range_B_refined5.62435.6433887
X-RAY DIFFRACTIONr_long_range_B_other5.62435.6523888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 149 -
Rwork0.303 2710 -
obs--97.44 %

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