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- PDB-6hdf: D170N variant of beta-phosphoglucomutase from Lactococcus lactis ... -

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Basic information

Entry
Database: PDB / ID: 6hdf
TitleD170N variant of beta-phosphoglucomutase from Lactococcus lactis in an open conformer to 1.4 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 / : / 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
Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsWood, H.P. / Robertson, 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 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)49,14414
Polymers48,4772
Non-polymers66712
Water5,224290
1
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5727
Polymers24,2391
Non-polymers3336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5727
Polymers24,2391
Non-polymers3336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.770, 119.310, 53.170
Angle α, β, γ (deg.)90.00, 94.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-phosphoglucomutase / Beta-PGM


Mass: 24238.607 Da / Num. of mol.: 2 / Mutation: K125R, Y206H, D170N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 24-34% PEG 4000 200mM sodium acetate 50mM TRIS pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.4→52.98 Å / Num. obs: 90031 / % possible obs: 95.4 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.055 / Rrim(I) all: 0.107 / Net I/σ(I): 8.2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4 % / Rmerge(I) obs: 1.243 / Num. unique obs: 4464 / CC1/2: 0.462 / Rpim(I) all: 0.701 / Rrim(I) all: 1.431 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WHE

2whe


Resolution: 1.4→52.98 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.285 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22352 4461 5 %RANDOM
Rwork0.17177 ---
obs0.1743 85527 95.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.439 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20.2 Å2
2--0.01 Å20 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.4→52.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 42 290 3710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0143528
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173335
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.6494763
X-RAY DIFFRACTIONr_angle_other_deg0.9771.6627813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4425451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50224.138174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19815625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.781516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023944
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02608
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_it1.9871.8231772
X-RAY DIFFRACTIONr_mcbond_other1.9861.8221771
X-RAY DIFFRACTIONr_mcangle_it2.4122.742218
X-RAY DIFFRACTIONr_mcangle_other2.4122.7412219
X-RAY DIFFRACTIONr_scbond_it2.9542.2171756
X-RAY DIFFRACTIONr_scbond_other2.9532.2171756
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4833.1682540
X-RAY DIFFRACTIONr_long_range_B_refined3.38922.2873719
X-RAY DIFFRACTIONr_long_range_B_other3.38922.2923720
X-RAY DIFFRACTIONr_rigid_bond_restr2.3236863
X-RAY DIFFRACTIONr_sphericity_free17.6355211
X-RAY DIFFRACTIONr_sphericity_bonded13.05656887
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 316 -
Rwork0.299 6342 -
obs--94.68 %

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