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- PDB-5ok1: D10N variant of beta-phosphoglucomutase from Lactococcus lactis t... -

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Basic information

Entry
Database: PDB / ID: 5ok1
TitleD10N variant of beta-phosphoglucomutase from Lactococcus lactis trapped with native beta-glucose 1,6-bisphosphate intermediate to 1.9A resolution.
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / bisphospho-intermediate
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 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily ...Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / : / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / 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
1,6-di-O-phosphono-beta-D-glucopyranose / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsRobertson, A.J. / Bisson, C.
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: Acs Catalysis / Year: 2018
Title: van der Waals Contact between Nucleophile and Transferring Phosphorus Is Insufficient To Achieve Enzyme Transition-State Architecture
Authors: Johnson, L.A. / Robertson, A.J. / Baxter, N.J. / Trevitt, C.R. / Bisson, C. / Jin, Y. / Wood, H.P. / Hounslow, A.M. / Cliff, M.J. / Blackburn, G.M. / Bowler, M.W. / Waltho, J.P.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.mon_nstd_flag / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 17, 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)24,2173
Polymers23,8521
Non-polymers3642
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Nuclear Magnetic Resonance (NMR) spectroscopy assignment of this complex. The linewidths and relaxation parameters of the backbone amides in this protein complex demonstrate a ...Evidence: homology, Nuclear Magnetic Resonance (NMR) spectroscopy assignment of this complex. The linewidths and relaxation parameters of the backbone amides in this protein complex demonstrate a monomeric species. GBP presence determined by 1H13C and 31P NMR experiments., homology, homology to previously deposited structures 1ZOL, 1O03, 1O08, 1Z4N, 1Z4O, 1LVH, 2WF5, 2WF6, 2WF7, 2WF8, 2WF9, 2WFA, 2WHE, 3FM9, 3ZI4, 4C4R, 4C4S, 4C4T
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.710, 74.490, 78.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-phosphoglucomutase / Beta-PGM


Mass: 23852.119 Da / Num. of mol.: 1 / Mutation: K125R, Y206H, D10N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (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 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-B16 / 1,6-di-O-phosphono-beta-D-glucopyranose / 1,6-di-O-phosphono-beta-D-glucose / 1,6-di-O-phosphono-D-glucose / 1,6-di-O-phosphono-glucose


Type: D-saccharide / Mass: 340.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Glcp1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 24-34% PEG 4000 200mM Tris pH 7.5 200mM sodium acetate harvested after ca. 12 weeks
PH range: 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.86→39.28 Å / Num. obs: 18807 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Net I/σ(I): 25.8
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.972 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 933 / CC1/2: 0.599 / Rpim(I) all: 0.558 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
MOLREPphasing
Coot0.8.1model building
XDSdata reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WF5

2wf5


Resolution: 1.86→39.28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.453 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24559 925 4.9 %RANDOM
Rwork0.19781 ---
obs0.20011 17834 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.719 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å20 Å2-0 Å2
2---1.31 Å20 Å2
3----1.29 Å2
Refinement stepCycle: 1 / Resolution: 1.86→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 21 67 1768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191739
X-RAY DIFFRACTIONr_bond_other_d0.0020.021688
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9882358
X-RAY DIFFRACTIONr_angle_other_deg0.94833902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0155219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.88625.65876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52315304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.281157
X-RAY DIFFRACTIONr_chiral_restr0.0760.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211947
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
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_it2.5274.116876
X-RAY DIFFRACTIONr_mcbond_other2.5254.111875
X-RAY DIFFRACTIONr_mcangle_it3.6576.1591095
X-RAY DIFFRACTIONr_mcangle_other3.6576.1651096
X-RAY DIFFRACTIONr_scbond_it2.724.388863
X-RAY DIFFRACTIONr_scbond_other2.7174.388863
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.226.4621264
X-RAY DIFFRACTIONr_long_range_B_refined5.85932.5461951
X-RAY DIFFRACTIONr_long_range_B_other5.85932.5471951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 61 -
Rwork0.311 1306 -
obs--99.93 %

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