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- PDB-7eq5: Plant growth-promoting factor YxaL mutant from Bacillus velezensi... -

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Basic information

Entry
Database: PDB / ID: 7eq5
TitlePlant growth-promoting factor YxaL mutant from Bacillus velezensis - T175W/W215G
ComponentsMembrane associated protein kinase with beta-propeller domain, pyrrolo-quinoline quinone beta-propeller repeat
KeywordsSIGNALING PROTEIN / beta-propeller / symbiotic / growth-promoting activity / Bacillus velezensis / Protein binding
Biological speciesBacillus velezensis FZB42 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKim, J. / Ha, N.-C.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structure of the plant growth-promoting factor YxaL from the rhizobacterium Bacillus velezensis and its application to protein engineering.
Authors: Kim, J. / Pham, H. / Baek, Y. / Jo, I. / Kim, Y.H. / Ha, N.C.
History
DepositionApr 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: 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: Membrane associated protein kinase with beta-propeller domain, pyrrolo-quinoline quinone beta-propeller repeat
B: Membrane associated protein kinase with beta-propeller domain, pyrrolo-quinoline quinone beta-propeller repeat


Theoretical massNumber of molelcules
Total (without water)88,2982
Polymers88,2982
Non-polymers00
Water00
1
A: Membrane associated protein kinase with beta-propeller domain, pyrrolo-quinoline quinone beta-propeller repeat


Theoretical massNumber of molelcules
Total (without water)44,1491
Polymers44,1491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Membrane associated protein kinase with beta-propeller domain, pyrrolo-quinoline quinone beta-propeller repeat


Theoretical massNumber of molelcules
Total (without water)44,1491
Polymers44,1491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.483, 176.483, 63.603
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Membrane associated protein kinase with beta-propeller domain, pyrrolo-quinoline quinone beta-propeller repeat


Mass: 44148.957 Da / Num. of mol.: 2 / Mutation: T175W, W215G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus velezensis FZB42 (bacteria) / Strain: FZB42 / Gene: HC661_36490 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium pH 7.0, 1.5 M Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 35219 / % possible obs: 100 % / Redundancy: 17.2 % / Biso Wilson estimate: 37.45 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.029 / Net I/σ(I): 23.88
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 1748 / CC1/2: 0.966 / Rpim(I) all: 0.074

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DXN

7dxn


Resolution: 2.6→48.89 Å / SU ML: 0.2821 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 20.9581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216 1687 4.79 %
Rwork0.1818 33532 -
obs0.1835 35219 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.95 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5601 0 0 0 5601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235749
X-RAY DIFFRACTIONf_angle_d0.50957847
X-RAY DIFFRACTIONf_chiral_restr0.0448859
X-RAY DIFFRACTIONf_plane_restr0.0041011
X-RAY DIFFRACTIONf_dihedral_angle_d5.6804792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.27921370.22982751X-RAY DIFFRACTION98.87
2.67-2.760.27381490.22122791X-RAY DIFFRACTION100
2.76-2.860.31471300.22582760X-RAY DIFFRACTION99.97
2.86-2.970.30421590.22792742X-RAY DIFFRACTION100
2.97-3.110.30691480.2452778X-RAY DIFFRACTION100
3.11-3.270.25511370.23222760X-RAY DIFFRACTION100
3.27-3.480.22871200.19672837X-RAY DIFFRACTION100
3.48-3.740.21171390.17952794X-RAY DIFFRACTION100
3.74-4.120.17991460.15672767X-RAY DIFFRACTION99.97
4.12-4.720.16171290.13332833X-RAY DIFFRACTION100
4.72-5.940.16161640.14692794X-RAY DIFFRACTION100
5.94-48.890.18071290.16512925X-RAY DIFFRACTION99.84

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