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- PDB-6k21: Pyrophosphatase from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 6k21
TitlePyrophosphatase from Acinetobacter baumannii
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / Pyrophosphatase from Acinetobacter baumannii
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
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 / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSu, J.
CitationJournal: Int J Mol Sci / Year: 2019
Title: Crystal Structures of Pyrophosphatase from Acinetobacter baumannii: Snapshots of Pyrophosphate Binding and Identification of a Phosphorylated Enzyme Intermediate.
Authors: Si, Y. / Wang, X. / Yang, G. / Yang, T. / Li, Y. / Ayala, G.J. / Li, X. / Wang, H. / Su, J.
History
DepositionMay 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5503
Polymers19,5031
Non-polymers472
Water3,711206
1
A: Inorganic pyrophosphatase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)117,30318
Polymers117,0196
Non-polymers28412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area14830 Å2
ΔGint-210 kcal/mol
Surface area39210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.813, 102.813, 100.776
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Inorganic pyrophosphatase / Pyrophosphate phospho-hydrolase / PPase


Mass: 19503.141 Da / Num. of mol.: 1 / Mutation: A139S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ppa / Production host: Escherichia coli (E. coli)
References: UniProt: N9S5K0, UniProt: A0A333SMX2*PLUS, inorganic diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Source detailsThe protein was from a strain of Acinetobacter baumannii from a hospital. The sequence reference ...The protein was from a strain of Acinetobacter baumannii from a hospital. The sequence reference used is from a different species Acinetobacter ursingii NIPH 706.

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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: 4.03 Å3/Da / Density % sol: 69.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→19.9 Å / Num. obs: 21726 / % possible obs: 99.8 % / Redundancy: 9.8 % / Net I/σ(I): 9
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1576

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Processing

SoftwareName: PHENIX / Version: 1.12_2829 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.897 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 2000 9.21 %
Rwork0.1752 19720 -
obs0.1786 21720 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.11 Å2 / Biso mean: 25.6826 Å2 / Biso min: 10.2 Å2
Refinement stepCycle: final / Resolution: 2→19.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 0 2 206 1550
Biso mean--47.25 34.8 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091377
X-RAY DIFFRACTIONf_angle_d0.9081879
X-RAY DIFFRACTIONf_chiral_restr0.061207
X-RAY DIFFRACTIONf_plane_restr0.005246
X-RAY DIFFRACTIONf_dihedral_angle_d2.925830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.23451390.191413751514100
2.05-2.10530.23911410.197613821523100
2.1053-2.16720.23511390.190313671506100
2.1672-2.23710.27861410.184714031544100
2.2371-2.31690.27311400.200813831523100
2.3169-2.40950.24551420.196113931535100
2.4095-2.5190.25821420.202313941536100
2.519-2.65150.25831410.211613951536100
2.6515-2.81720.24961430.211401154499
2.8172-3.0340.23871410.195214011542100
3.034-3.33810.20761440.175914221566100
3.3381-3.81810.19311450.149114321577100
3.8181-4.79930.16041470.13041443159099
4.7993-19.89790.16571550.16761529168498

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