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- PDB-8jgu: Crystal structure of N-terminal domain of exopolyphosphatase from... -

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Basic information

Entry
Database: PDB / ID: 8jgu
TitleCrystal structure of N-terminal domain of exopolyphosphatase from Deinococcus radiodurans
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
Biological speciesDeinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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)35,8372
Polymers35,8141
Non-polymers231
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.410, 101.410, 49.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

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Components

#1: Protein Exopolyphosphatase


Mass: 35814.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal domain of wild-type protein
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-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.04 Å3/Da / Density % sol: 39.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NaAc

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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: Jul 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 19639 / % possible obs: 98 % / Redundancy: 7.05 % / CC1/2: 0.993 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.12 / Net I/σ(I): 17.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.99-2.040.5714100.780.6261
2.04-2.10.63414030.7040.7061
2.1-2.160.39913980.8090.4421
2.16-2.220.35813400.890.3931
2.22-2.30.43213030.7580.4761
2.3-2.380.26412600.8950.2891
2.38-2.470.22112290.9450.2421
2.47-2.570.20611750.9410.2261
2.57-2.680.18611180.940.2051
2.68-2.810.13710600.9510.151
2.81-2.970.11810050.990.1291
2.97-3.150.0969610.990.1061
3.15-3.360.0778920.9940.0841
3.36-3.630.0698340.9950.0741
3.63-3.980.0667640.9930.0721
3.98-4.450.0587100.9950.0631
4.45-5.140.0616120.990.0671
5.14-6.290.0555190.9950.061
6.29-8.90.0544130.9980.0581
8.9-300.0462330.9960.0491

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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: 1.99→29.27 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 953 4.86 %
Rwork0.1841 --
obs0.1856 19612 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 1 172 2461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.824
X-RAY DIFFRACTIONf_dihedral_angle_d12.791863
X-RAY DIFFRACTIONf_chiral_restr0.05359
X-RAY DIFFRACTIONf_plane_restr0.01427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.090.2541440.21572606X-RAY DIFFRACTION97
2.1-2.230.24161380.18462678X-RAY DIFFRACTION100
2.23-2.40.24331280.20232708X-RAY DIFFRACTION99
2.4-2.640.2181430.20212665X-RAY DIFFRACTION99
2.64-3.020.22871300.2012656X-RAY DIFFRACTION98
3.02-3.80.2071330.17372658X-RAY DIFFRACTION97
3.81-29.270.1831370.16492688X-RAY DIFFRACTION96

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