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- PDB-4c4s: Structure of beta-phosphoglucomutase in complex with an alpha- fl... -

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Basic information

Entry
Database: PDB / ID: 4c4s
TitleStructure of beta-phosphoglucomutase in complex with an alpha- fluorophosphonate analogue of beta-glucose-1-phosphate and magnesium trifluoride
ComponentsBETA-PHOSPHOGLUCOMUTASE
KeywordsISOMERASE / PHOSPHORYL TRANSFER / TRANSITION STATE / METAL FLUORIDE / MUTASE
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-GRX / TRIFLUOROMAGNESATE / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPellegrini, E. / Bowler, M.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Alpha-Fluorophosphonates Reveal How a Phosphomutase Conserves Transition State Conformation Over Hexose Recognition in its Two-Step Reaction.
Authors: Jin, Y. / Bhattasali, D. / Pellegrini, E. / Forget, S.M. / Baxter, N.J. / Cliff, M.J. / Bowler, M.W. / Jakeman, D.L. / Blackburn, G.M. / Waltho, J.P.
History
DepositionSep 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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_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_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: 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)24,6214
Polymers24,2401
Non-polymers3823
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.541, 54.337, 104.346
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: 24239.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P71447, beta-phosphoglucomutase
#2: Sugar ChemComp-GRX / (1R)-1,5-anhydro-1-[(S)-fluoro(phosphono)methyl]-D-glucitol / (S)-1-beta-phosphonofluoromethylene-1-deoxy-D-glucopyranose


Type: D-saccharide / Mass: 276.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14FO8P
#3: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F3Mg
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Description: DATA WERE COLLECTED USING THE GROB ROBOT GONIOMETER
Crystal growpH: 7.2
Details: 27-32% PEG 4000, 50-75 MM MAGNESIUM ACETATE, pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2011 / Details: TOROIDAL MIRROR
RadiationMonochromator: C001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→52.2 Å / Num. obs: 33872 / % possible obs: 97.1 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.2 / % possible all: 88.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WF5

2wf5


Resolution: 1.5→37.634 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 18.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1984 1692 5 %
Rwork0.1725 --
obs0.1738 33820 96.58 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.199 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso mean: 12.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.0974 Å20 Å20 Å2
2---5.97 Å20 Å2
3---1.8726 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 22 296 1974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131723
X-RAY DIFFRACTIONf_angle_d1.4242346
X-RAY DIFFRACTIONf_dihedral_angle_d12.972639
X-RAY DIFFRACTIONf_chiral_restr0.131267
X-RAY DIFFRACTIONf_plane_restr0.007301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54420.27261140.2242212X-RAY DIFFRACTION81
1.5442-1.5940.23851440.21262571X-RAY DIFFRACTION95
1.594-1.6510.22461410.18352705X-RAY DIFFRACTION98
1.651-1.71710.20681350.17312679X-RAY DIFFRACTION98
1.7171-1.79520.21621480.17832686X-RAY DIFFRACTION99
1.7952-1.88990.24651240.16712732X-RAY DIFFRACTION99
1.8899-2.00830.24841340.17252718X-RAY DIFFRACTION99
2.0083-2.16330.17451450.17012706X-RAY DIFFRACTION99
2.1633-2.3810.17841540.15922707X-RAY DIFFRACTION98
2.381-2.72550.18581300.15942758X-RAY DIFFRACTION98
2.7255-3.43340.18731540.17342785X-RAY DIFFRACTION99
3.4334-37.64550.18591690.17192869X-RAY DIFFRACTION97

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