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- PDB-8jgq: Crystal structure of Deinococcus radiodurans exopolyphosphatase c... -

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Basic information

Entry
Database: PDB / ID: 8jgq
TitleCrystal structure of Deinococcus radiodurans exopolyphosphatase complexed with P5
ComponentsExopolyphosphatase
KeywordsHYDROLASE / Polyphosphate / exopolyphosphatase
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 / HD/PDEase domain / ATPase, nucleotide binding domain
Similarity search - Domain/homology
: / Exopolyphosphatase
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhao, Y. / Dai, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170028 China
CitationJournal: Adv Sci / Year: 2024
Title: Structural Evolution of Bacterial Polyphosphate Degradation Enzyme for Phosphorus Cycling.
Authors: Dai, S. / Wang, B. / Ye, R. / Zhang, D. / Xie, Z. / Yu, N. / Cai, C. / Huang, C. / Zhao, J. / Zhang, F. / Hua, Y. / Zhao, Y. / Zhou, R. / Tian, B.
History
DepositionMay 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8509
Polymers56,8311
Non-polymers1,0198
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-15 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.710, 166.710, 39.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Exopolyphosphatase


Mass: 56831.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Gene: DR_A0185 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RYW9
#2: Chemical ChemComp-UG3 / bis[oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate


Mass: 417.915 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H7O16P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: NaAc, NH4SO4, polyp, Mg2+

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 20832 / % possible obs: 94.4 % / Redundancy: 3.05 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.084 / Net I/σ(I): 11.69
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.5-2.570.52915880.7130.6371
2.57-2.640.43815160.8170.5281
2.64-2.710.35714950.8550.431
2.71-2.80.28114190.9070.3381
2.8-2.890.23613740.9370.2841
2.89-2.990.17213070.960.2091
2.99-3.10.1312750.9710.1611
3.1-3.230.11112510.9860.1331
3.23-3.380.08911670.9870.1071
3.38-3.540.08211440.990.0971
3.54-3.730.0710160.9920.0871
3.73-3.960.05710270.9950.0691
3.96-4.230.0539560.9950.0631
4.23-4.570.0478670.9950.0571
4.57-5.010.0428090.9960.051
5.01-5.60.0437220.9960.0521
5.6-6.460.0416330.9970.051
6.46-7.920.0355700.9970.0421
7.92-11.190.034510.9970.0361
11.19-300.0312450.9970.0381

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.88 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 1018 4.89 %
Rwork0.2118 --
obs0.2136 20798 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3629 0 52 32 3713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.901
X-RAY DIFFRACTIONf_dihedral_angle_d13.4571353
X-RAY DIFFRACTIONf_chiral_restr0.051571
X-RAY DIFFRACTIONf_plane_restr0.011678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.32041430.28872890X-RAY DIFFRACTION97
2.63-2.80.34271430.26232858X-RAY DIFFRACTION96
2.8-3.020.27631330.26412821X-RAY DIFFRACTION95
3.02-3.320.29371510.25152816X-RAY DIFFRACTION95
3.32-3.80.30051480.22142760X-RAY DIFFRACTION93
3.8-4.780.19381620.16852790X-RAY DIFFRACTION93
4.79-28.880.20431380.18162845X-RAY DIFFRACTION91

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