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- PDB-8jgx: Crystal structure of Acinetobacter baumannii exopolyphosphatase -

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Basic information

Entry
Database: PDB / ID: 8jgx
TitleCrystal structure of Acinetobacter baumannii exopolyphosphatase
ComponentsExopolyphosphatase
KeywordsHYDROLASE / Polyphosphate / exopolyphosphatase
Function / homology:
Function and homology information
Biological speciesAcinetobacter baumannii 15827 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
B: Exopolyphosphatase


Theoretical massNumber of molelcules
Total (without water)117,7462
Polymers117,7462
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.220, 160.500, 81.440
Angle α, β, γ (deg.)90.00, 96.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exopolyphosphatase


Mass: 58872.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii 15827 (bacteria)
Gene: ppx, AB237_2873 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E1PV46, exopolyphosphatase

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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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: NH4Ac, BIS-TRIS, PEG 3350

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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: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 34012 / % possible obs: 97.8 % / Redundancy: 3.69 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.063 / Net I/σ(I): 15.97
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.6-2.660.55922910.9160.661
2.66-2.740.39224150.9210.4691
2.74-2.820.30724260.9460.3571
2.82-2.90.21923590.9750.2541
2.9-30.16822850.9830.1951
3-3.10.13122270.9880.1521
3.1-3.220.11221360.990.131
3.22-3.350.09419870.990.1131
3.35-3.50.07818590.9920.0931
3.5-3.670.05618630.9940.0671
3.67-3.870.0517460.9960.0591
3.87-4.110.04416050.9950.0531
4.11-4.390.03916060.9980.0451
4.39-4.740.03714740.9970.0431
4.74-5.190.03513720.9980.0411
5.19-5.810.03612370.9980.0421
5.81-6.70.03610950.9980.0421
6.7-8.210.0329340.9980.0371
8.21-11.610.0277240.9980.0321
11.61-300.0263710.9990.031

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.36 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2759 1688 4.97 %
Rwork0.2251 --
obs0.2277 33978 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7613 0 0 0 7613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.015
X-RAY DIFFRACTIONf_dihedral_angle_d14.7722824
X-RAY DIFFRACTIONf_chiral_restr0.061184
X-RAY DIFFRACTIONf_plane_restr0.0091360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.43021160.38172426X-RAY DIFFRACTION89
2.67-2.760.41431560.3172737X-RAY DIFFRACTION99
2.76-2.860.3931540.30792677X-RAY DIFFRACTION99
2.86-2.970.29741260.2692775X-RAY DIFFRACTION100
2.97-3.110.33051420.25752747X-RAY DIFFRACTION100
3.11-3.270.34161360.27822692X-RAY DIFFRACTION98
3.27-3.470.39341260.28462658X-RAY DIFFRACTION97
3.48-3.740.2661480.23542658X-RAY DIFFRACTION97
3.74-4.120.2461510.21932626X-RAY DIFFRACTION96
4.12-4.710.24631340.17722763X-RAY DIFFRACTION100
4.71-5.930.22941310.20112769X-RAY DIFFRACTION100
5.93-29.360.22491680.17132762X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.4641 Å / Origin y: -11.0941 Å / Origin z: -10.451 Å
111213212223313233
T0.3133 Å2-0.0231 Å20.0241 Å2-0.3712 Å2-0.0375 Å2--0.4329 Å2
L1.391 °2-0.5675 °20.5235 °2-1.3038 °2-0.3688 °2--0.9475 °2
S-0.1081 Å °-0.0565 Å °0.3041 Å °0.0334 Å °0.0578 Å °-0.0478 Å °-0.1736 Å °-0.0293 Å °0.0525 Å °
Refinement TLS groupSelection details: all

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