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- PDB-7f3n: Structure of PopP2 in apo form -

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Basic information

Entry
Database: PDB / ID: 7f3n
TitleStructure of PopP2 in apo form
ComponentsType III effector protein popp2
KeywordsTRANSFERASE / YopJ / PopP2 / acetyltransferase
Function / homologySerine/Threonine acetyltransferase, YopJ / YopJ Serine/Threonine acetyltransferase / acyltransferase activity / Type III effector protein popp2
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35185590332 Å
AuthorsXia, Y. / Zhang, Z.M.
CitationJournal: Nat Commun / Year: 2021
Title: Secondary-structure switch regulates the substrate binding of a YopJ family acetyltransferase.
Authors: Xia, Y. / Zou, R. / Escouboue, M. / Zhong, L. / Zhu, C. / Pouzet, C. / Wu, X. / Wang, Y. / Lv, G. / Zhou, H. / Sun, P. / Ding, K. / Deslandes, L. / Yuan, S. / Zhang, Z.M.
History
DepositionJun 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type III effector protein popp2


Theoretical massNumber of molelcules
Total (without water)37,7391
Polymers37,7391
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12890 Å2
Unit cell
Length a, b, c (Å)89.36, 89.36, 79.871
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-525-

HOH

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Components

#1: Protein Type III effector protein popp2


Mass: 37738.668 Da / Num. of mol.: 1 / Fragment: UNP residues 149-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (strain GMI1000) (bacteria)
Strain: GMI1000 / Gene: popP2, RSc0868 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y125
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 Hepeps, pH7.5, 50 mM MgCl2, 30% PEG55OMME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 15654 / % possible obs: 100 % / Redundancy: 9.2 % / CC1/2: 0.984 / Net I/σ(I): 15.9
Reflection shellResolution: 2.35→2.43 Å / Num. unique obs: 1503 / CC1/2: 0.898

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-2000data scaling
Cootmodel building
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W3T

5w3t


Resolution: 2.35185590332→35.4887640895 Å / SU ML: 0.254941632031 / Cross valid method: FREE R-VALUE / σ(F): 1.38062729577 / Phase error: 24.4818682495
RfactorNum. reflection% reflection
Rfree0.231361943868 1562 9.98976720389 %
Rwork0.19293203813 14074 -
obs0.196863902294 15636 99.82761923 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.7970177276 Å2
Refinement stepCycle: LAST / Resolution: 2.35185590332→35.4887640895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 0 34 1887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003781958386511880
X-RAY DIFFRACTIONf_angle_d0.7752542113992543
X-RAY DIFFRACTIONf_chiral_restr0.0275224075521296
X-RAY DIFFRACTIONf_plane_restr0.00387596262214338
X-RAY DIFFRACTIONf_dihedral_angle_d15.382475487696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3519-2.42770.2997510454481360.2699853890551225X-RAY DIFFRACTION100
2.4277-2.51450.303362255951380.2440376256211266X-RAY DIFFRACTION99.9288256228
2.5145-2.61510.2662615279981390.2477921831181283X-RAY DIFFRACTION100
2.6151-2.73410.2558242802381360.2553503439271257X-RAY DIFFRACTION99.8566308244
2.7341-2.87820.3195277894121420.238182438331281X-RAY DIFFRACTION99.9297752809
2.8782-3.05840.2919745075841410.2412797738991264X-RAY DIFFRACTION100
3.0584-3.29440.265565112591470.2369081565921267X-RAY DIFFRACTION99.7882851094
3.2944-3.62570.2229199781171440.2061579903071288X-RAY DIFFRACTION99.8605299861
3.6257-4.14960.2114710287521440.1647119598721280X-RAY DIFFRACTION99.7198879552
4.1496-5.22540.183799312531460.146995181461309X-RAY DIFFRACTION99.9313186813
5.2254-35.480.214524890211490.1670082717431354X-RAY DIFFRACTION99.1424802111
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.73169225970.592597666188-1.346931781582.21808118446-2.485109107965.36390758173-0.5136874599970.8436247110020.596187495226-0.3105442330250.771525985392-0.02691660348430.07063158137541.057827688510.3267561997930.658587255432-0.424295565358-0.1174879503330.4736978817020.1339404707380.481873415919-19.9025546149196.5327665238.27259545924
22.46268850298-0.3319972335870.9604505297065.448488311951.561308648594.91069603490.120339164672-0.153376279683-0.0482868483975-0.6960694029050.3776660272941.08461344966-0.378814132616-0.468487475972-0.2085991913630.549054524931-0.153653232578-0.2045887157540.3916818235460.1513946674980.560300312142-37.2545250337186.66348527112.4314787463
35.68895715542-1.01850705107-0.8506943904173.08230360051.656097117371.88540669846-1.10325960185-0.278547823559-0.1300366396920.3622150823450.451034437091.01643872468-0.2259470810140.000798696231247-0.2180149573390.705669934398-0.178554081316-0.2000400143820.4466340349310.1797262749150.649009792429-39.7973062152173.52269143815.8103198081
43.391093437121.81998136295-1.017671967765.191377220080.2344338968781.821554424730.1788879981660.0877066580818-0.501528721656-0.3950435825060.4829231220980.2825161442930.795564263638-0.0247021615714-0.1553187130.793264670452-0.205189072988-0.3130652586060.3497694983060.09732193227810.540560642038-32.4370744134174.53157327710.5589602152
53.02667837041.354834606151.269752794284.231020432780.04553357576872.12726887823-0.2773544392250.505276157207-0.0130070896393-0.7575451053270.8676019148810.2325601696060.4121185154560.250271397988-0.3301439025050.798117165375-0.188075760936-0.1752428475460.552257238790.09709646455580.414498483001-27.9784303457183.504718336.31557822358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 146 through 208 )
2X-RAY DIFFRACTION2chain 'A' and (resid 209 through 268 )
3X-RAY DIFFRACTION3chain 'A' and (resid 269 through 305 )
4X-RAY DIFFRACTION4chain 'A' and (resid 306 through 351 )
5X-RAY DIFFRACTION5chain 'A' and (resid 352 through 484 )

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