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- PDB-5ojz: D10N variant of beta-phosphoglucomutase from Lactococcus lactis i... -

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Basic information

Entry
Database: PDB / ID: 5ojz
TitleD10N variant of beta-phosphoglucomutase from Lactococcus lactis inhibited by a beryllium triflouride phosphoenzyme analogue to 1.3A resolution.
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / phosphoenzyme analogue
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
BERYLLIUM TRIFLUORIDE ION / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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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)24,84514
Polymers24,1091
Non-polymers73513
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Nuclear Magnetic Resonance (NMR) spectroscopy assignment of this complex in the wild type enzyme. The linewidths and relaxation parameters of the backbone amides in this protein ...Evidence: homology, Nuclear Magnetic Resonance (NMR) spectroscopy assignment of this complex in the wild type enzyme. The linewidths and relaxation parameters of the backbone amides in this protein complex are consistent with a monomeric species. 19F NMR was used to confirm the presence of BeF3 in the active site., 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 area2130 Å2
ΔGint20 kcal/mol
Surface area11100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.760, 53.800, 81.550
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: 24109.430 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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
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
PH range: 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.3→44.3 Å / Num. obs: 57228 / % possible obs: 99 % / Redundancy: 16.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Net I/σ(I): 16.1
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2525 / CC1/2: 0.489 / Rpim(I) all: 0.542 / % possible all: 88.3

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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: 2WHE

2whe


Resolution: 1.3→44.3 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.793 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.043 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16952 2843 5 %RANDOM
Rwork0.13564 ---
obs0.13721 54322 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2---0.18 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.3→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 46 244 1988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191790
X-RAY DIFFRACTIONr_bond_other_d0.0020.021780
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9862402
X-RAY DIFFRACTIONr_angle_other_deg0.94634109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2645225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.44325.71477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11715317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.109157
X-RAY DIFFRACTIONr_chiral_restr0.1750.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211995
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02366
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_it1.4921.607894
X-RAY DIFFRACTIONr_mcbond_other1.491.601893
X-RAY DIFFRACTIONr_mcangle_it1.952.4141121
X-RAY DIFFRACTIONr_mcangle_other1.952.421122
X-RAY DIFFRACTIONr_scbond_it2.5042.013896
X-RAY DIFFRACTIONr_scbond_other2.5052.012896
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9212.8541282
X-RAY DIFFRACTIONr_long_range_B_refined3.78915.222211
X-RAY DIFFRACTIONr_long_range_B_other3.78815.2262212
X-RAY DIFFRACTIONr_rigid_bond_restr2.00633570
X-RAY DIFFRACTIONr_sphericity_free32.727573
X-RAY DIFFRACTIONr_sphericity_bonded9.68553723
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 187 -
Rwork0.271 3599 -
obs--90.12 %

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