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- PDB-6h92: Phosphorylated beta-phosphoglucomutase from Lactococcus lactis in... -

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Basic information

Entry
Database: PDB / ID: 6h92
TitlePhosphorylated beta-phosphoglucomutase from Lactococcus lactis in an open conformer to 2.6 A
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / phospho-enzyme / phospho-aspartate / acetylphosphate
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
ACETYLPHOSPHATE / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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)48,8265
Polymers48,6392
Non-polymers1873
Water99155
1
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3442
Polymers24,3201
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4833
Polymers24,3201
Non-polymers1632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.410, 117.180, 52.980
Angle α, β, γ (deg.)90.00, 98.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-phosphoglucomutase / Beta-PGM


Mass: 24319.574 Da / Num. of mol.: 2 / Mutation: K125R, Y206H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-UVW / ACETYLPHOSPHATE


Mass: 140.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5O5P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 49.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 24-34% PEG 4000, 200 mM sodium acetate, 50 mM TRIS pH 7.5. Crystals were cryoprotected in their initial mother liquor plus an additional 25% ethylene glycol and 30 mM acetylphosphate.
PH range: 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→47.82 Å / Num. obs: 14087 / % possible obs: 98.5 % / Redundancy: 3.7 % / CC1/2: 0.958 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.142 / Rrim(I) all: 0.272 / Net I/σ(I): 5
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.829 / Num. unique obs: 1042 / CC1/2: 0.499 / Rpim(I) all: 0.584 / Rrim(I) all: 1.153 / % possible all: 99.4

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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: 2.6→47.82 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.823 / SU B: 21.1 / SU ML: 0.431 / Cross valid method: THROUGHOUT / ESU R Free: 0.427 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31601 741 5.3 %RANDOM
Rwork0.23342 ---
obs0.23788 13324 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.428 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å20.64 Å2
2--1.74 Å2-0 Å2
3----1.74 Å2
Refinement stepCycle: 1 / Resolution: 2.6→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 10 55 3433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193435
X-RAY DIFFRACTIONr_bond_other_d0.0020.023271
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9834652
X-RAY DIFFRACTIONr_angle_other_deg0.97437606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8335434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.9325.6150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52115600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.371514
X-RAY DIFFRACTIONr_chiral_restr0.0730.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213806
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02636
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_it1.9714.1231742
X-RAY DIFFRACTIONr_mcbond_other1.9694.1231741
X-RAY DIFFRACTIONr_mcangle_it3.246.1832174
X-RAY DIFFRACTIONr_mcangle_other3.246.1842175
X-RAY DIFFRACTIONr_scbond_it1.8084.3011693
X-RAY DIFFRACTIONr_scbond_other1.8074.3021694
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0526.3612479
X-RAY DIFFRACTIONr_long_range_B_refined5.0849.093742
X-RAY DIFFRACTIONr_long_range_B_other5.07249.13740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 50 -
Rwork0.347 989 -
obs--99.43 %

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