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- PDB-8jgr: Crystal structure of Deinococcus radiodurans exopolyphosphatase i... -

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Basic information

Entry
Database: PDB / ID: 8jgr
TitleCrystal structure of Deinococcus radiodurans exopolyphosphatase in the presence of Pi
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
: / PHOSPHATE ION / 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)57,2897
Polymers56,8311
Non-polymers4586
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-22 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.010, 165.010, 39.170
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: NaH2PO4, K2HPO4

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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: May 30, 2020
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: 20449 / % possible obs: 94.4 % / Redundancy: 5.94 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.067 / Net I/σ(I): 17.76
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.5-2.560.54815320.8460.591
2.56-2.630.43314720.9030.4671
2.63-2.710.33914250.9420.3671
2.71-2.790.28914210.9590.311
2.79-2.890.23213360.9710.251
2.89-2.990.18213330.9830.1961
2.99-3.10.14712520.9890.1591
3.1-3.230.10712420.9940.1151
3.23-3.370.08311800.9950.091
3.37-3.530.06511250.9970.071
3.53-3.730.05710320.9970.0621
3.73-3.950.04610000.9980.0491
3.95-4.220.0429360.9980.0461
4.22-4.560.0388680.9980.0411
4.56-50.0397900.9980.0421
5-5.590.0437220.9980.0461
5.59-6.450.0446230.9970.0481
6.45-7.90.0375370.9980.041
7.9-11.180.0384090.9980.0411
11.18-300.0372140.9990.041

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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→28.58 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 973 4.76 %
Rwork0.2203 --
obs0.2215 20444 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 22 16 3592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.869
X-RAY DIFFRACTIONf_dihedral_angle_d12.7281308
X-RAY DIFFRACTIONf_chiral_restr0.049564
X-RAY DIFFRACTIONf_plane_restr0.012665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.31651550.27852785X-RAY DIFFRACTION96
2.63-2.80.2871150.25862814X-RAY DIFFRACTION96
2.8-3.010.27141590.25662779X-RAY DIFFRACTION96
3.01-3.310.29871330.25582820X-RAY DIFFRACTION96
3.31-3.790.27171330.22232785X-RAY DIFFRACTION95
3.79-4.770.23031410.19112762X-RAY DIFFRACTION93
4.78-28.580.19871370.20262726X-RAY DIFFRACTION89

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