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- PDB-7poe: Phosphoglycolate Phosphatase with Inhibitor CP1 -

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Basic information

Entry
Database: PDB / ID: 7poe
TitlePhosphoglycolate Phosphatase with Inhibitor CP1
ComponentsGlycerol-3-phosphate phosphatase
KeywordsHYDROLASE / PGP / Glycerol-3-phosphate phosphatase / AUM / Inhibitor
Function / homology
Function and homology information


glycerol-3-phosphatase activity / glycerol-1-phosphatase / glycerol-1-phosphatase activity / glycerophospholipid metabolic process / phosphoglycolate phosphatase activity / ADP phosphatase activity / glycerol biosynthetic process / negative regulation of gluconeogenesis / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...glycerol-3-phosphatase activity / glycerol-1-phosphatase / glycerol-1-phosphatase activity / glycerophospholipid metabolic process / phosphoglycolate phosphatase activity / ADP phosphatase activity / glycerol biosynthetic process / negative regulation of gluconeogenesis / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / magnesium ion binding / cytoplasm
Similarity search - Function
2-phosphoglycolate phosphatase, eukaryotic / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Chem-7VK / : / Glycerol-3-phosphate phosphatase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsSchloetzer, J. / Fratz, S. / Schindelin, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Glycolytic flux control by drugging phosphoglycolate phosphatase.
Authors: Jeanclos, E. / Schlotzer, J. / Hadamek, K. / Yuan-Chen, N. / Alwahsh, M. / Hollmann, R. / Fratz, S. / Yesilyurt-Gerhards, D. / Frankenbach, T. / Engelmann, D. / Keller, A. / Kaestner, A. / ...Authors: Jeanclos, E. / Schlotzer, J. / Hadamek, K. / Yuan-Chen, N. / Alwahsh, M. / Hollmann, R. / Fratz, S. / Yesilyurt-Gerhards, D. / Frankenbach, T. / Engelmann, D. / Keller, A. / Kaestner, A. / Schmitz, W. / Neuenschwander, M. / Hergenroder, R. / Sotriffer, C. / von Kries, J.P. / Schindelin, H. / Gohla, A.
History
DepositionSep 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jul 3, 2024Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerol-3-phosphate phosphatase
B: Glycerol-3-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,42210
Polymers69,1212
Non-polymers2,3018
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-27 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.902, 105.902, 83.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLYGLYchain 'A'AA11 - 32111 - 321
127VK7VK7VK7VKchain 'A'AC401
13GOLGOLGOLGOLchain 'A'AE403
21ALAALAGLYGLY(chain 'B' and (resid 11 through 321 or resid 401 or resid 403 or resid 601))BB11 - 32111 - 321
227VK7VK7VK7VK(chain 'B' and (resid 11 through 321 or resid 401 or resid 403 or resid 601))BF401
23GOLGOLGOLGOL(chain 'B' and (resid 11 through 321 or resid 401 or resid 403 or resid 601))BH403

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Components

#1: Protein Glycerol-3-phosphate phosphatase / G3PP / Aspartate-based ubiquitous Mg(2+)-dependent phosphatase / AUM / Phosphoglycolate phosphatase / PGP


Mass: 34560.559 Da / Num. of mol.: 2 / Mutation: D34N, C297S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pgp / Production host: Escherichia coli (E. coli)
References: UniProt: Q8CHP8, glycerol-1-phosphatase, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-7VK / 2-[[4-[4-[(2-carboxyphenyl)carbamoyl]phenoxy]phenyl]carbonylamino]benzoic acid


Mass: 496.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H20N2O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.33 Å3/Da / Density % sol: 63.14 % / Description: Prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.49 M NaH2PO4 0.91 K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.16→47.36 Å / Num. obs: 12387 / % possible obs: 82.19 % / Redundancy: 7.8 % / Biso Wilson estimate: 95.32 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.082 / Net I/σ(I): 7.94
Reflection shellResolution: 3.16→3.38 Å / Rmerge(I) obs: 2.334 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 651 / CC1/2: 0.3022 / Rpim(I) all: 0.869

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PO7

7po7


Resolution: 3.16→47.36 Å / SU ML: 0.3823 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0923 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2449 609 4.69 %
Rwork0.2117 12377 -
obs0.2132 12986 81.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.74 Å2
Refinement stepCycle: LAST / Resolution: 3.16→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4712 0 167 2 4881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00334971
X-RAY DIFFRACTIONf_angle_d0.73276743
X-RAY DIFFRACTIONf_chiral_restr0.0464752
X-RAY DIFFRACTIONf_plane_restr0.00461008
X-RAY DIFFRACTIONf_dihedral_angle_d19.25643066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.480.3623660.31051320X-RAY DIFFRACTION35.07
3.48-3.980.28971830.25763445X-RAY DIFFRACTION91.82
3.98-5.020.23211810.20653768X-RAY DIFFRACTION99.72
5.02-47.360.22081790.1883844X-RAY DIFFRACTION99.65

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