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- PDB-6pc2: Crystal structure of Helicobacter pylori PPX/GppA in complex with GNP -

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Basic information

Entry
Database: PDB / ID: 6pc2
TitleCrystal structure of Helicobacter pylori PPX/GppA in complex with GNP
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / PHOSPHATE ION / Guanosine pentaphosphate phosphohydrolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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)112,83312
Polymers111,3112
Non-polymers1,52110
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-96 kcal/mol
Surface area37850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.016, 94.475, 107.197
Angle α, β, γ (deg.)90.00, 108.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M Potassium chloride

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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 MX300-HS / Detector: CCD / Date: Jun 10, 2016
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 23947 / % possible obs: 100 % / Redundancy: 7.6 % / Rpim(I) all: 0.055 / Net I/σ(I): 13.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2375 / % possible all: 100

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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: 2.9→35.884 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.06
RfactorNum. reflection% reflection
Rfree0.3099 1999 8.35 %
Rwork0.2535 --
obs0.2582 23929 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→35.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7614 0 88 14 7716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027838
X-RAY DIFFRACTIONf_angle_d0.49510556
X-RAY DIFFRACTIONf_dihedral_angle_d9.8944826
X-RAY DIFFRACTIONf_chiral_restr0.0411222
X-RAY DIFFRACTIONf_plane_restr0.0051288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8931-2.96550.38541380.35041504X-RAY DIFFRACTION96
2.9655-3.04560.41121420.36651559X-RAY DIFFRACTION100
3.0456-3.13520.45311420.36221570X-RAY DIFFRACTION100
3.1352-3.23630.48011420.36391550X-RAY DIFFRACTION100
3.2363-3.35190.4551450.33761587X-RAY DIFFRACTION100
3.3519-3.4860.37671420.32071554X-RAY DIFFRACTION100
3.486-3.64450.40051410.32191558X-RAY DIFFRACTION100
3.6445-3.83640.38421430.3071559X-RAY DIFFRACTION100
3.8364-4.07650.34681430.28431581X-RAY DIFFRACTION100
4.0765-4.39070.31061440.2581575X-RAY DIFFRACTION100
4.3907-4.83160.31351410.22431548X-RAY DIFFRACTION100
4.8316-5.52860.26311450.22991578X-RAY DIFFRACTION100
5.5286-6.95710.25921430.23611585X-RAY DIFFRACTION100
6.9571-35.88680.21011480.16881622X-RAY DIFFRACTION99

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