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- PDB-8hoe: Apo structure of HopBF1 kinase from Ewingella americana -

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Basic information

Entry
Database: PDB / ID: 8hoe
TitleApo structure of HopBF1 kinase from Ewingella americana
ComponentsType III effector HopBF1
KeywordsTRANSFERASE / Kinase
Function / homologyType III effector HopBF1
Function and homology information
Biological speciesEwingella americana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, C.C. / Xu, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Apo structure of HopBF1 kinase from Ewingella americana
Authors: Wang, C.C.
History
DepositionDec 9, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type III effector HopBF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5737
Polymers21,1671
Non-polymers4066
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.283, 134.283, 124.163
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"

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Components

#1: Protein Type III effector HopBF1


Mass: 21166.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ewingella americana (bacteria) / Gene: GEAM_1328 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A085GHR3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 5.08 Å3/Da / Density % sol: 75.78 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 2 M ammonium sulfate, 8 % (V/V) ethylene glycol, ,10 % (w/v) PEG 8000, 0.1 M HEPES sodium pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.2→38.76 Å / Num. obs: 21950 / % possible obs: 99.96 % / Redundancy: 19.2 % / Biso Wilson estimate: 58.63 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.016 / Rrim(I) all: 0.069 / Net I/σ(I): 23.88
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 1.441 / Num. unique obs: 2681 / CC1/2: 0.755 / CC star: 0.928 / Rpim(I) all: 0.348

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIXdev_4778refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.76 Å / SU ML: 0.3332 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.1306
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2253 1086 4.95 %
Rwork0.1984 20865 -
obs0.1998 21950 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.34 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 25 31 1430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121417
X-RAY DIFFRACTIONf_angle_d1.12551906
X-RAY DIFFRACTIONf_chiral_restr0.0648214
X-RAY DIFFRACTIONf_plane_restr0.0093253
X-RAY DIFFRACTIONf_dihedral_angle_d12.2653534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.32881380.31842544X-RAY DIFFRACTION100
2.3-2.420.29211410.27732576X-RAY DIFFRACTION100
2.42-2.570.31471300.25262613X-RAY DIFFRACTION100
2.57-2.770.30771450.26712584X-RAY DIFFRACTION100
2.77-3.050.2541110.24522615X-RAY DIFFRACTION100
3.05-3.490.28271440.22722599X-RAY DIFFRACTION100
3.49-4.40.18981430.16492630X-RAY DIFFRACTION99.96
4.4-38.760.17741340.16392704X-RAY DIFFRACTION99.75

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