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- PDB-4c4r: Structure of beta-phosphoglucomutase in complex with a phosphonat... -

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Basic information

Entry
Database: PDB / ID: 4c4r
TitleStructure of beta-phosphoglucomutase in complex with a phosphonate 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 / 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
TRIFLUOROMAGNESATE / (1R)-1,5-anhydro-1-(phosphonomethyl)-D-glucitol / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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.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_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_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

Downloads & links

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Assembly

Deposited unit
A: BETA-PHOSPHOGLUCOMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6034
Polymers24,2401
Non-polymers3643
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.012, 54.201, 105.407
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 / BETAPHOSPHOGLUCOMUTASE


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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-YO5 / (1R)-1,5-anhydro-1-(phosphonomethyl)-D-glucitol / Beta-1 phosphonomethylene-D-glucopyranose


Type: D-saccharide / Mass: 258.163 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H15O8P
#4: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F3Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.27 Å3/Da / Density % sol: 45.3 % / Description: NONE
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: ID29 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2012 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.1→52.7 Å / Num. obs: 82900 / % possible obs: 93.1 % / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Biso Wilson estimate: 5.37 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.7
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.9 / % possible all: 85.7

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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: 1.1→19.648 Å / SU ML: 0.1 / σ(F): 1.35 / Phase error: 14.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1726 4136 5 %
Rwork0.1492 --
obs0.1504 82621 92.64 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.384 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 6.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.6794 Å20 Å20 Å2
2---2.4107 Å20 Å2
3---3.0902 Å2
Refinement stepCycle: LAST / Resolution: 1.1→19.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 21 566 2264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111769
X-RAY DIFFRACTIONf_angle_d1.3622412
X-RAY DIFFRACTIONf_dihedral_angle_d12.144655
X-RAY DIFFRACTIONf_chiral_restr0.07271
X-RAY DIFFRACTIONf_plane_restr0.008312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11250.22571120.21292309X-RAY DIFFRACTION83
1.1125-1.12560.19641190.18692386X-RAY DIFFRACTION85
1.1256-1.13930.22331150.16872409X-RAY DIFFRACTION86
1.1393-1.15370.16171300.15472439X-RAY DIFFRACTION86
1.1537-1.16890.16791130.14522423X-RAY DIFFRACTION88
1.1689-1.18490.18771280.1442511X-RAY DIFFRACTION89
1.1849-1.20190.17211130.14812508X-RAY DIFFRACTION89
1.2019-1.21980.171270.14762433X-RAY DIFFRACTION88
1.2198-1.23880.17261290.13552513X-RAY DIFFRACTION90
1.2388-1.25920.14671240.12412581X-RAY DIFFRACTION92
1.2592-1.28090.15571320.1242562X-RAY DIFFRACTION92
1.2809-1.30420.161360.13532586X-RAY DIFFRACTION92
1.3042-1.32920.15581350.13112618X-RAY DIFFRACTION94
1.3292-1.35640.17651400.12982629X-RAY DIFFRACTION93
1.3564-1.38580.16481570.13242590X-RAY DIFFRACTION94
1.3858-1.41810.16931400.12922637X-RAY DIFFRACTION94
1.4181-1.45350.14121550.12622657X-RAY DIFFRACTION95
1.4535-1.49280.18571520.13472615X-RAY DIFFRACTION94
1.4928-1.53670.16961390.12942707X-RAY DIFFRACTION95
1.5367-1.58630.16051500.1332677X-RAY DIFFRACTION95
1.5863-1.6430.17661490.12882718X-RAY DIFFRACTION96
1.643-1.70870.1551320.13922668X-RAY DIFFRACTION95
1.7087-1.78640.17861390.14492734X-RAY DIFFRACTION96
1.7864-1.88050.16191750.15062705X-RAY DIFFRACTION96
1.8805-1.99830.16161460.14442727X-RAY DIFFRACTION96
1.9983-2.15240.17171450.15422771X-RAY DIFFRACTION97
2.1524-2.36860.1461290.14872746X-RAY DIFFRACTION95
2.3686-2.71060.19471620.16692807X-RAY DIFFRACTION98
2.7106-3.41220.15311410.15712870X-RAY DIFFRACTION98
3.4122-19.65070.20891720.17682949X-RAY DIFFRACTION97

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