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- PDB-2bqx: Inorganic Pyrophosphatase from the Pathogenic Bacterium Helicobac... -

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Basic information

Entry
Database: PDB / ID: 2bqx
TitleInorganic Pyrophosphatase from the Pathogenic Bacterium Helicobacter pylori-Kinetic and Structural Properties
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsHYDROLASE / INORGANIC PYROPHOSPHATASE / HELICOBACTER PYLORI
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytosol
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Inorganic pyrophosphatase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChao, T.-C. / Sun, Y.-J.
CitationJournal: Proteins / Year: 2006
Title: Kinetic and Structural Properties of Inorganic Pyrophosphatase from the Pathogenic Bacterium Helicobacter Pylori.
Authors: Chao, T.-C. / Huang, H. / Tsai, J.Y. / Huang, C.Y. / Sun, Y.-J.
History
DepositionApr 28, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INORGANIC PYROPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)19,2981
Polymers19,2981
Non-polymers00
Water3,441191
1
A: INORGANIC PYROPHOSPHATASE
x 6


Theoretical massNumber of molelcules
Total (without water)115,7886
Polymers115,7886
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation12_565x,x-y+1,-z+1/21
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)102.650, 102.650, 93.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2016-

HOH

21A-2052-

HOH

31A-2181-

HOH

41A-2187-

HOH

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Components

#1: Protein INORGANIC PYROPHOSPHATASE / PYROPHOSPHATE PHOSPHO-HYDROLASE / PPASE


Mass: 19297.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG13009 / References: UniProt: P56153, inorganic diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.44 Å3/Da / Density % sol: 64 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→19.93 Å / Num. obs: 192336 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.1
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.36 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QEZ

1qez


Resolution: 1.9→19.93 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 355817.05 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1094 4.8 %RANDOM
Rwork0.217 ---
obs0.217 22676 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.5299 Å2 / ksol: 0.384942 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.49 Å20 Å2
2--0.32 Å20 Å2
3----0.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 0 191 1492
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it2.582
X-RAY DIFFRACTIONc_scangle_it3.642.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 157 4.4 %
Rwork0.233 3439 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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