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- PDB-8gty: Crystal structure of exopolyphosphatase (PPX) from Zymomonas mobi... -

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Basic information

Entry
Database: PDB / ID: 8gty
TitleCrystal structure of exopolyphosphatase (PPX) from Zymomonas mobilis in complex with magnesium ions
ComponentsPpx/GppA phosphatase
KeywordsMETAL BINDING PROTEIN / Polyphosphate / PPX/GppA
Function / homology
Function and homology information


pyrophosphatase activity / metal ion binding
Similarity search - Function
: / Exopolyphosphatase, C-terminal / : / Ppx/GppA phosphatase / Ppx/GppA phosphatase family / Exopolyphosphatase. Domain 2 / Hypothetical protein af1432 / Hypothetical protein af1432 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain ...: / Exopolyphosphatase, C-terminal / : / Ppx/GppA phosphatase / Ppx/GppA phosphatase family / Exopolyphosphatase. Domain 2 / Hypothetical protein af1432 / Hypothetical protein af1432 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ppx/GppA phosphatase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLu, Z. / Wang, J. / Zhang, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structure of the exopolyphosphatase (PPX) from Zymomonas mobilis reveals a two-magnesium-ions PPX.
Authors: Lu, Z. / Hu, Y. / Wang, J. / Zhang, B. / Zhang, Y. / Cui, Z. / Zhang, L. / Zhang, A.
History
DepositionSep 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 2.0Mar 27, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / reflns / reflns_shell / software / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.pdbx_number_of_molecules / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_residues_total / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _software.classification / _software.name / _software.version
Description: Ligand identity / Provider: author / Type: Coordinate replacement
Revision 2.1May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ppx/GppA phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5243
Polymers53,4761
Non-polymers492
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-20 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.023, 47.118, 89.480
Angle α, β, γ (deg.)90.00, 124.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ppx/GppA phosphatase


Mass: 53475.598 Da / Num. of mol.: 1 / Mutation: I169V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
Strain: ATCC 31821 / ZM4 / Gene: ZMO0713 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5NPM3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 1.98 Å3/Da / Density % sol: 37.98 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 50 mM Tris pH 8.0, 500 mM NaCl, 5% glycerol 0.2 M magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 25%(w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→43.84 Å / Num. obs: 36563 / % possible obs: 92.65 % / Redundancy: 4 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.065 / Rrim(I) all: 0.136 / Χ2: 0.921 / Net I/σ(I): 8.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.515 / Num. unique obs: 2697 / CC1/2: 0.645 / CC star: 0.886 / Rpim(I) all: 0.336 / Rrim(I) all: 0.62 / Χ2: 0.765 / % possible all: 67.4

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HI0

3hi0


Resolution: 1.8→41.51 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 -5.07 %
Rwork0.1998 --
obs-34708 92.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 2 246 3934
LS refinement shellResolution: 1.8→1.84 Å /
RfactorNum. reflection
Rfree0.2761 80
Rwork0.2031 -

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