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- PDB-9m0m: Crystal structure of a thermophilic family II inorganic pyrophosp... -

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Basic information

Entry
Database: PDB / ID: 9m0m
TitleCrystal structure of a thermophilic family II inorganic pyrophosphatase in Thermodesulfobacterium commune
Componentsinorganic diphosphatase
KeywordsCYTOSOLIC PROTEIN / inorganic pyrophosphatase
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / metal ion binding / cytoplasm
Similarity search - Function
DHHA2 domain / DHHA2 domain superfamily / DHHA2 domain / DHHA2 / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily
Similarity search - Domain/homology
: / inorganic diphosphatase
Similarity search - Component
Biological speciesThermodesulfobacterium commune (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsMaruoka, S. / Teramoto, T. / Watanabe, K. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23KJ1741 Japan
CitationJournal: To Be Published
Title: Crystal structure of a thermophilic family II inorganic pyrophosphatase enabling high-temperature adaptation in Thermodesulfobacterium commune
Authors: Maruoka, S. / Teramoto, T. / Watanabe, K. / Kakuta, Y.
History
DepositionFeb 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: inorganic diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7079
Polymers35,0821
Non-polymers6258
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-11 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.070, 66.070, 451.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein inorganic diphosphatase / Pyrophosphate phospho-hydrolase


Mass: 35081.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermodesulfobacterium commune (bacteria)
Gene: DCE01_05400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A101FK03, inorganic diphosphatase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.05 Å3/Da / Density % sol: 69.64 %
Crystal growTemperature: 294.3 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→48.32 Å / Num. obs: 36790 / % possible obs: 99.1 % / Redundancy: 17.01 % / CC1/2: 0.998 / Net I/σ(I): 37.72
Reflection shellResolution: 2.08→2.21 Å / Num. unique obs: 3679 / CC1/2: 0.616

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→48.32 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 2000 5.44 %
Rwork0.1878 --
obs0.1896 36790 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 33 216 2709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022697
X-RAY DIFFRACTIONf_angle_d0.4523657
X-RAY DIFFRACTIONf_dihedral_angle_d13.9571024
X-RAY DIFFRACTIONf_chiral_restr0.043427
X-RAY DIFFRACTIONf_plane_restr0.003465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.45131390.39752427X-RAY DIFFRACTION100
2.13-2.190.33081380.32862394X-RAY DIFFRACTION100
2.19-2.250.32181370.28192390X-RAY DIFFRACTION100
2.25-2.330.3281390.24312425X-RAY DIFFRACTION100
2.33-2.410.27641400.23582419X-RAY DIFFRACTION100
2.41-2.510.25681400.2332445X-RAY DIFFRACTION100
2.51-2.620.30091410.2422443X-RAY DIFFRACTION100
2.62-2.760.32041420.25462478X-RAY DIFFRACTION100
2.76-2.930.26261410.23112437X-RAY DIFFRACTION100
2.93-3.160.24081430.20762492X-RAY DIFFRACTION100
3.16-3.480.21961450.2092517X-RAY DIFFRACTION100
3.48-3.980.21321440.16622505X-RAY DIFFRACTION100
3.98-5.010.16791490.14512601X-RAY DIFFRACTION100
5.01-48.320.19771620.16682817X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -35.7629 Å / Origin y: -41.5324 Å / Origin z: 16.1808 Å
111213212223313233
T0.3515 Å20.0047 Å20.0128 Å2-0.5791 Å2-0.1188 Å2--0.4976 Å2
L2.4405 °2-1.2962 °22.2956 °2-1.2821 °2-1.8503 °2--3.1676 °2
S0.1246 Å °0.3038 Å °0.0308 Å °-0.1323 Å °-0.1658 Å °0.0522 Å °0.3457 Å °0.1114 Å °0.0544 Å °
Refinement TLS groupSelection details: all

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