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- PDB-6pc0: Crystal structure of Helicobacter pylori PPX/GppA -

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Basic information

Entry
Database: PDB / ID: 6pc0
TitleCrystal structure of Helicobacter pylori PPX/GppA
ComponentsGuanosine pentaphosphate phosphohydrolase
KeywordsHYDROLASE / pppGpp / ppGpp / PPX / GppA / Polyphosphate
Function / homology
Function and homology information


pyrophosphatase activity / metal ion binding
Similarity search - Function
Pyrophosphatase, GppA/Ppx-type / : / Ppx/GppA phosphatase, domain III / : / Ppx/GppA phosphatase / Ppx/GppA phosphatase family / ATPase, nucleotide binding domain
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / D-MALATE / Guanosine pentaphosphate phosphohydrolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSong, H. / Wang, C. / Shaw, G.X. / Ji, X.
CitationJournal: Febs J. / Year: 2020
Title: Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori.
Authors: Song, H. / Dharmasena, M.N. / Wang, C. / Shaw, G.X. / Cherry, S. / Tropea, J.E. / Jin, D.J. / Ji, X.
History
DepositionJun 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Guanosine pentaphosphate phosphohydrolase
B: Guanosine pentaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,51937
Polymers111,3112
Non-polymers3,20835
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-288 kcal/mol
Surface area38680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.362, 129.458, 166.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Guanosine pentaphosphate phosphohydrolase


Mass: 55655.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: HPG27_257 / Production host: Escherichia coli (E. coli) / References: UniProt: B5ZA44

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Non-polymers , 5 types, 707 molecules

#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#5: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350 (v/v), 0.2 M Ammonium sulfate, 15 mM Malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 1, 2014
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 120859 / % possible obs: 99.2 % / Redundancy: 6.4 % / Rpim(I) all: 0.036 / Net I/σ(I): 17.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 11705 / Rpim(I) all: 0.428 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(dev_3352: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hi0

3hi0


Resolution: 1.7→39.112 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.66
RfactorNum. reflection% reflection
Rfree0.2124 1000 0.82 %
Rwork0.1888 --
obs0.1891 122528 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→39.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7589 0 182 672 8443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088153
X-RAY DIFFRACTIONf_angle_d1.26811002
X-RAY DIFFRACTIONf_dihedral_angle_d10.5274972
X-RAY DIFFRACTIONf_chiral_restr0.0681256
X-RAY DIFFRACTIONf_plane_restr0.0091354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6949-1.78430.33751340.300616309X-RAY DIFFRACTION94
1.7843-1.89610.26621420.251417132X-RAY DIFFRACTION98
1.8961-2.04250.21841420.210817326X-RAY DIFFRACTION99
2.0425-2.2480.26291430.194717426X-RAY DIFFRACTION100
2.248-2.57320.24371440.199417550X-RAY DIFFRACTION100
2.5732-3.24180.23311460.205317680X-RAY DIFFRACTION100
3.2418-39.12240.17371490.162618105X-RAY DIFFRACTION99

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