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- PDB-6h8v: Beta-phosphoglucomutase from Lactococcus lactis in an open confor... -

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Basic information

Entry
Database: PDB / ID: 6h8v
TitleBeta-phosphoglucomutase from Lactococcus lactis in an open conformer in the P21 spacegroup to 1.8 A.
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase
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
1,3-PROPANDIOL / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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)48,6666
Polymers48,4792
Non-polymers1874
Water7,170398
1
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4024
Polymers24,2401
Non-polymers1623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2642
Polymers24,2401
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.100, 53.710, 81.090
Angle α, β, γ (deg.)90.00, 90.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
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
PH range: 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.84→44.29 Å / Num. obs: 33973 / % possible obs: 85.5 % / Redundancy: 2.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.063 / Rrim(I) all: 0.11 / Net I/σ(I): 10.2
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2605 / CC1/2: 0.556 / Rpim(I) all: 0.503 / Rrim(I) all: 0.87 / % possible all: 89.3

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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: 1.84→44.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.96 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23562 1644 4.8 %RANDOM
Rwork0.18596 ---
obs0.18841 32325 85.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.169 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å2-0 Å2-0.12 Å2
2---0.55 Å2-0 Å2
3----0.91 Å2
Refinement stepCycle: 1 / Resolution: 1.84→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 11 398 3769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193446
X-RAY DIFFRACTIONr_bond_other_d0.0020.023290
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9764662
X-RAY DIFFRACTIONr_angle_other_deg0.96337654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.16125.714154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15815605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.551514
X-RAY DIFFRACTIONr_chiral_restr0.0890.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213838
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02640
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_it1.2961.9351752
X-RAY DIFFRACTIONr_mcbond_other1.2961.9341751
X-RAY DIFFRACTIONr_mcangle_it1.9052.8952190
X-RAY DIFFRACTIONr_mcangle_other1.9042.8972191
X-RAY DIFFRACTIONr_scbond_it1.8792.2131694
X-RAY DIFFRACTIONr_scbond_other1.8782.2131694
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.933.2062473
X-RAY DIFFRACTIONr_long_range_B_refined4.24224.1363976
X-RAY DIFFRACTIONr_long_range_B_other4.24224.1453977
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 125 -
Rwork0.28 2476 -
obs--89.14 %

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