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

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Basic information

Entry
Database: PDB / ID: 8jgp
TitleCrystal structure of Deinococcus radiodurans exopolyphosphatase complexed with pyrophosphate
ComponentsExopolyphosphatase
KeywordsHYDROLASE / Polyphosphate / exopolyphosphatase / pyrophosphate
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 / PYROPHOSPHATE / Exopolyphosphatase
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 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)57,3516
Polymers56,8311
Non-polymers5205
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-13 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.250, 168.250, 39.840
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-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: NaAc, NH4SO4, polyp, Mn2+

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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: Nov 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.02→30 Å / Num. obs: 12294 / % possible obs: 93.6 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.106 / Net I/σ(I): 8.75
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.02-3.090.3938850.9170.4741
3.09-3.180.3619080.9360.4241
3.18-3.270.3499110.9440.4051
3.27-3.370.358760.9480.4041
3.37-3.480.3978070.9220.4641
3.48-3.610.9657070.8821.1281
3.61-3.740.16810.9860.1221
3.74-3.890.2996270.9640.3541
3.89-4.070.1316270.9790.1581
4.07-4.270.1026900.9880.121
4.27-4.50.096790.990.1061
4.5-4.770.0746150.9930.0871
4.77-5.10.0695770.9950.081
5.1-5.510.0655360.9940.0771
5.51-6.030.0564970.9960.0671
6.03-6.740.0494690.9960.0571
6.74-7.790.044140.9980.0461
7.79-9.540.0453570.9960.0521
9.54-13.490.0422860.9970.0491
13.49-300.0371450.9960.0451

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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: 3.02→29.14 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.317 568 4.71 %
Rwork0.2641 --
obs0.2667 12059 91.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.02→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 25 0 3594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.487
X-RAY DIFFRACTIONf_dihedral_angle_d12.6081308
X-RAY DIFFRACTIONf_chiral_restr0.077572
X-RAY DIFFRACTIONf_plane_restr0.014666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.320.37321530.33672997X-RAY DIFFRACTION97
3.32-3.80.4886940.43082515X-RAY DIFFRACTION81
3.8-4.780.33681450.27842903X-RAY DIFFRACTION93
4.79-29.140.25861760.19063076X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 29.5833 Å / Origin y: -53.378 Å / Origin z: 0.6143 Å
111213212223313233
T0.6116 Å2-0.0303 Å20.1341 Å2-0.4838 Å20.0098 Å2--0.6774 Å2
L4.1599 °2-0.1418 °20.5054 °2-1.0114 °20.1506 °2--1.0207 °2
S0.0513 Å °-0.2686 Å °0.5598 Å °0.1488 Å °-0.0197 Å °0.319 Å °-0.1068 Å °-0.1454 Å °-0.0351 Å °
Refinement TLS groupSelection details: all

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