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- PDB-6z0p: BceF Tyrosine Kinase Domain -

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Basic information

Entry
Database: PDB / ID: 6z0p
TitleBceF Tyrosine Kinase Domain
ComponentsBceF
KeywordsTRANSFERASE / bacterial tyrosine kinase / bcef / biofilm / Burkholderia cepacia / exopolysaccharide biosynthesis
Function / homology
Function and homology information


: / protein tyrosine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Tyrosine kinase, G-rich domain / G-rich domain on putative tyrosine kinase / Exopolysaccharide synthesis protein / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / : / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BceF
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
Model detailsBceF
AuthorsLandau, M. / Mayer, M. / Abd Alhadi, M. / Dvir, H.
CitationJournal: Biomolecules / Year: 2021
Title: Structural and Functional Insights into the Biofilm-Associated BceF Tyrosine Kinase Domain from Burkholderia cepacia .
Authors: Mayer, M. / Matiuhin, Y. / Nawatha, M. / Tabachnikov, O. / Fish, I. / Schutz, N. / Dvir, H. / Landau, M.
History
DepositionMay 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: 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: BceF
B: BceF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7844
Polymers58,9302
Non-polymers8542
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Size exclusion chromatography- multi angle light scattering (SEC-MALS)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-15 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.270, 90.480, 61.340
Angle α, β, γ (deg.)90.000, 111.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BceF


Mass: 29464.916 Da / Num. of mol.: 2 / Fragment: BceF kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Gene: bceF / Plasmid: pET11d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0GYW2
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 0.1M Bis-Tris pH 5.5, 25% polyethylene glycol 3350, 3% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.596
11H, -K, -H-L20.404
ReflectionResolution: 1.85→48.36 Å / Num. obs: 38309 / % possible obs: 99.4 % / Redundancy: 3.715 % / Biso Wilson estimate: 30.76 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.112 / Χ2: 0.943 / Net I/σ(I): 9.55 / Num. measured all: 142307
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.85-2.23.7620.4732.735822815548154780.8060.55199.5
2.2-2.83.7270.1727.54374011799117370.9650.20199.5
2.8-3.63.7040.06916.2421603587658330.9930.08199.3
3.6-4.63.5770.03925.489719274227170.9970.04699.1
4.6-5.83.4460.03626.94346127512610.9980.04398.9
5.8-7.23.5990.03826.2521816136060.9970.04498.9
7.2-8.83.8160.0331.3311603063040.9990.03599.3
8.8-103.9030.0334.194411171130.9990.03496.6
10-303.4780.02532.698732532510.9990.0399.2
30-48.361.7780.0223.85161090.9970.02690

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO / Packing: 0
Highest resolutionLowest resolution
Rotation1.85 Å19.88 Å
Translation1.85 Å19.88 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.5.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CIO

3cio


Resolution: 1.85→48.36 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.224 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 1895 4.9 %RANDOM
Rwork0.1825 ---
obs0.1835 36413 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.73 Å2 / Biso mean: 23.6 Å2 / Biso min: 12.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å2-2.82 Å2
2--9.48 Å20 Å2
3----7.49 Å2
Refinement stepCycle: final / Resolution: 1.85→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3675 0 54 51 3780
Biso mean--20.62 24.83 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133788
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173701
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.6495138
X-RAY DIFFRACTIONr_angle_other_deg1.4091.5748561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0145480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.87720.053187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99815660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7851540
X-RAY DIFFRACTIONr_chiral_restr0.0620.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02763
LS refinement shellResolution: 1.85→1.897 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.235 147 -
Rwork0.256 2609 -
obs--96.6 %

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