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- PDB-6qzg: Beta-glucose 1,6-bisphosphonate bound to wild type beta-phosphogl... -

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Basic information

Entry
Database: PDB / ID: 6qzg
TitleBeta-glucose 1,6-bisphosphonate bound to wild type beta-phosphoglucomutse in an open conformation.
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / synthetic phosphorane inhibitor / 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 / 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
Chem-JLT / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsRobertson, A.J.
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: Beta-glucose 1,6-bisphosphonate bound to wild type beta-phosphoglucomutse in an open conformation.
Authors: Robertson, A.J. / Waltho, J.P.
History
DepositionMar 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2006
Polymers48,4792
Non-polymers7214
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Homologous to the glucose 1,6-bisphospate complex in the D10N variant (PDB: 5ok1). Heteronuclear NMR was performed to confirm the binding interaction in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-17 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.270, 117.330, 52.780
Angle α, β, γ (deg.)90.00, 97.78, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain 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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-JLT / 3,7-anhydro-1,2,8-trideoxy-1,8-diphosphono-D-glycero-D-gulo-octitol / [(2~{S},3~{S},4~{R},5~{R},6~{S})-3,4,5-tris(oxidanyl)-6-(2-phosphonoethyl)oxan-2-yl]methylphosphonic acid


Type: D-saccharide / Mass: 336.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O10P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 49.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 24-34% PEG 4000 50 mM TRIS ph 7.5 200 mM sodium acetate

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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: 2.47→58.67 Å / Num. obs: 16554 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.082 / Rrim(I) all: 0.162 / Net I/σ(I): 8.1
Reflection shellResolution: 2.47→2.53 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1221 / CC1/2: 0.47 / Rpim(I) all: 0.559 / Rrim(I) all: 1.12 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WHE

2whe


Resolution: 2.47→58.66 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.867 / SU B: 12.567 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.785 / ESU R Free: 0.334 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27827 832 5 %RANDOM
Rwork0.19301 ---
obs0.19723 15698 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.377 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20.63 Å2
2---0.89 Å2-0 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.47→58.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 42 142 3562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133498
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173327
X-RAY DIFFRACTIONr_angle_refined_deg1.621.6574745
X-RAY DIFFRACTIONr_angle_other_deg1.2441.67752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0285436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.0524.337166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29115610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2111514
X-RAY DIFFRACTIONr_chiral_restr0.0660.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02652
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_it3.0864.191750
X-RAY DIFFRACTIONr_mcbond_other3.0874.1891749
X-RAY DIFFRACTIONr_mcangle_it4.5816.2832184
X-RAY DIFFRACTIONr_mcangle_other4.586.2842185
X-RAY DIFFRACTIONr_scbond_it3.9064.6931748
X-RAY DIFFRACTIONr_scbond_other3.8864.6861737
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9576.842562
X-RAY DIFFRACTIONr_long_range_B_refined7.96949.4783730
X-RAY DIFFRACTIONr_long_range_B_other7.97249.4773730
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.47→2.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 60 -
Rwork0.286 1156 -
obs--100 %

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