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- PDB-5o6p: Structure of beta-phosphoglucomutase D10N mutant in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5o6p
TitleStructure of beta-phosphoglucomutase D10N mutant in complex with glucose-1,6-bisphosphate
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoryl transfer / catalysis / near attack complex
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
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: 2.2 Å
AuthorsBowler, M.W.
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
DepositionJun 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 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

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Assembly

Deposited unit
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6033
Polymers24,2391
Non-polymers3642
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.750, 68.300, 83.230
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: 24238.609 Da / Num. of mol.: 1 / Mutation: D10N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1.86 Å3/Da / Density % sol: 33.93 %
Description: small needles with approximate dimensions 0.03 mm x 0.05 mm x 0.5 mm
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 28-32 % PEG 4000 and 100 mM Na acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 30, 2009 / Details: toroidla mirror
RadiationMonochromator: C001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 31189 / % possible obs: 98.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4 / Num. unique obs: 4563 / Rpim(I) all: 0.17 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wf9

2wf9


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.032 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.251 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25683 452 4.8 %RANDOM
Rwork0.19777 ---
obs0.20074 9024 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.635 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å2-0 Å20 Å2
2--1.87 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 21 70 1702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021659
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2241.992247
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.475207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.54525.35271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.68415289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.637157
X-RAY DIFFRACTIONr_chiral_restr0.1420.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211216
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6871.444834
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1342.1621039
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7751.515825
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.77520.6172610
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 31 -
Rwork0.247 661 -
obs--99.43 %
Refinement TLS params.Method: refined / Origin x: -13.5909 Å / Origin y: -8.523 Å / Origin z: 11.695 Å
111213212223313233
T0.0851 Å20.0357 Å2-0.0144 Å2-0.098 Å2-0.0279 Å2--0.0342 Å2
L4.5809 °2-0.9688 °2-0.8983 °2-3.3902 °2-0.5772 °2--4.6945 °2
S0.2265 Å °0.4495 Å °-0.0257 Å °-0.2331 Å °-0.0485 Å °0.2388 Å °-0.4652 Å °-0.0081 Å °-0.178 Å °

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