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

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Basic information

Entry
Database: PDB / ID: 7evf
TitlePlant growth-promoting factor YxaL mutant from Bacillus velezensis - T175W/S213G/W215A
ComponentsPQQ_3 domain-containing protein
KeywordsSIGNALING PROTEIN / beta-propeller / symbiotic / growth-promoting activity / Bacillus velezensis / Protein binding
Function / homologyBeta-alanine-activating enzyme, beta-propeller / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Pyrrolo-quinoline quinone repeat / Outer membrane protein assembly factor BamB / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / WD40/YVTN repeat-like-containing domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesBacillus velezensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionMay 21, 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
AA: PQQ_3 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)39,8971
Polymers39,8971
Non-polymers00
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.987, 152.987, 61.694
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein PQQ_3 domain-containing protein


Mass: 39896.891 Da / Num. of mol.: 1 / Mutation: T175W, S191P, S213G, W215A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / FZB42) (bacteria)
Strain: DSM 23117 / BGSC 10A6 / FZB42 / Gene: RBAM_036900 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A7ZAJ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 3.48 Å3/Da / Density % sol: 64.68 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium citrate pH 5.8, 16% (w/v) PEG 4000, 20% (v/v) Isopropanol

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 84369 / % possible obs: 98.1 % / Redundancy: 8.3 % / Biso Wilson estimate: 12.67 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.02 / Net I/σ(I): 33
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 4.9 / Num. unique obs: 4087 / CC1/2: 0.94 / CC star: 0.984 / Rpim(I) all: 0.116 / Rrim(I) all: 0.32

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DXN

7dxn


Resolution: 1.5→38.88 Å / SU ML: 0.1115 / Cross valid method: FREE R-VALUE / σ(F): 2.25 / Phase error: 13.9402
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1648 4143 4.93 %
Rwork0.1498 79812 -
obs0.1505 83955 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.87 Å2
Refinement stepCycle: LAST / Resolution: 1.5→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 0 291 3108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972911
X-RAY DIFFRACTIONf_angle_d1.08253979
X-RAY DIFFRACTIONf_chiral_restr0.0737436
X-RAY DIFFRACTIONf_plane_restr0.0085514
X-RAY DIFFRACTIONf_dihedral_angle_d7.1222406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.22921400.20132322X-RAY DIFFRACTION87.12
1.52-1.540.21531540.19552504X-RAY DIFFRACTION91.81
1.54-1.550.20621330.18252500X-RAY DIFFRACTION93.1
1.55-1.570.17941540.18292618X-RAY DIFFRACTION95.09
1.57-1.590.20231180.16992648X-RAY DIFFRACTION95.71
1.6-1.620.19051440.16662593X-RAY DIFFRACTION96.24
1.62-1.640.15451500.1592609X-RAY DIFFRACTION96.98
1.64-1.660.18591410.15742646X-RAY DIFFRACTION96.74
1.66-1.690.17871280.15592671X-RAY DIFFRACTION97.73
1.69-1.720.15931340.15142676X-RAY DIFFRACTION96.86
1.72-1.750.1571440.15482634X-RAY DIFFRACTION97.64
1.75-1.780.18031190.14392706X-RAY DIFFRACTION98.26
1.78-1.810.171230.15722679X-RAY DIFFRACTION97.06
1.81-1.850.18561270.14942697X-RAY DIFFRACTION98.5
1.85-1.890.15931420.14492688X-RAY DIFFRACTION98.26
1.89-1.940.15291470.1442650X-RAY DIFFRACTION97.9
1.94-1.980.17541550.14532688X-RAY DIFFRACTION98.72
1.98-2.040.15181320.14142680X-RAY DIFFRACTION99.33
2.04-2.10.17051540.1452669X-RAY DIFFRACTION98.91
2.1-2.160.1661480.14242731X-RAY DIFFRACTION98.9
2.16-2.240.17091210.14372678X-RAY DIFFRACTION99.04
2.24-2.330.17141400.14222729X-RAY DIFFRACTION99.27
2.33-2.440.15771350.14862715X-RAY DIFFRACTION99.44
2.44-2.570.17911270.15532723X-RAY DIFFRACTION99.2
2.57-2.730.17271300.15832736X-RAY DIFFRACTION99.58
2.73-2.940.17831570.16172722X-RAY DIFFRACTION99.76
2.94-3.230.16541450.1632710X-RAY DIFFRACTION99.9
3.23-3.70.14751310.1472714X-RAY DIFFRACTION99.86
3.7-4.660.13581540.12812723X-RAY DIFFRACTION99.93
4.66-38.880.14491160.13592753X-RAY DIFFRACTION99.97

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