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- PDB-6i03: D10N variant of beta-phosphoglucomutase from Lactococcus lactis c... -

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Basic information

Entry
Database: PDB / ID: 6i03
TitleD10N variant of beta-phosphoglucomutase from Lactococcus lactis complexed with tetrafluoroaluminate and beta-G6P to 1.02 A
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / metal fluoride / transition state analog
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 / 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 / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / 6-O-phosphono-beta-D-glucopyranose / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsRobertson, A.J. / 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: Proton transfer modulates the electrostatic environment in a general acid-base catalyzed phosphoryl transfer reaction
Authors: Robertson, A.J. / Bisson, C. / Waltho, J.P.
History
DepositionOct 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6755
Polymers24,2651
Non-polymers4104
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Homology to previously deposited PDB files 2WF6 and 5OK2. Furthermore, NMR spectroscopy was used to confirm the presence of the complex with tetrafluoroaluminate and glucose 6-phosphate.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-17 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.520, 54.280, 104.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Beta-phosphoglucomutase / / Beta-PGM


Mass: 24264.646 Da / Num. of mol.: 1 / Mutation: D10N, 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
#3: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 234 molecules

#2: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / 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: 1.02→37.52 Å / Num. obs: 106736 / % possible obs: 97.6 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Net I/σ(I): 16.1
Reflection shellResolution: 1.02→1.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.917 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6606 / CC1/2: 0.542 / Rpim(I) all: 0.589 / Rrim(I) all: 1.209 / % possible all: 82.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WF6

2wf6


Resolution: 1.02→35.33 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.055 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1747 5373 5 %RANDOM
Rwork0.15147 ---
obs0.15265 101274 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.192 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2---0.97 Å2-0 Å2
3---0.46 Å2
Refinement stepCycle: 1 / Resolution: 1.02→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 23 231 1946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132022
X-RAY DIFFRACTIONr_bond_other_d0.0050.0171909
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.6452751
X-RAY DIFFRACTIONr_angle_other_deg1.521.5884452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31724.21996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84915346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.779158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022288
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02380
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_it1.9121.3421035
X-RAY DIFFRACTIONr_mcbond_other1.8561.3391034
X-RAY DIFFRACTIONr_mcangle_it1.9742.0181302
X-RAY DIFFRACTIONr_mcangle_other2.0652.0241303
X-RAY DIFFRACTIONr_scbond_it2.1371.556987
X-RAY DIFFRACTIONr_scbond_other2.1381.556987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3922.2511450
X-RAY DIFFRACTIONr_long_range_B_refined2.63116.4832019
X-RAY DIFFRACTIONr_long_range_B_other2.45115.9821962
X-RAY DIFFRACTIONr_rigid_bond_restr24.17233930
X-RAY DIFFRACTIONr_sphericity_free19.1275140
X-RAY DIFFRACTIONr_sphericity_bonded24.74453984
LS refinement shellResolution: 1.02→1.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 330 -
Rwork0.33 6273 -
obs--82.3 %

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