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- PDB-4xhp: Bacillus thuringiensis ParM hybrid protein with ADP, containing t... -

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Basic information

Entry
Database: PDB / ID: 4xhp
TitleBacillus thuringiensis ParM hybrid protein with ADP, containing two ParM mutants
ComponentsParM hybrid fusion protein
KeywordsSTRUCTURAL PROTEIN / BACTERIAL ACTIN-LIKE PROTEIN / BACTERIAL CYTOSKELETON
Function / homologyActin-like protein, N-terminal / Actin like proteins N terminal domain / ParM-like / ATPase, nucleotide binding domain / ATP binding / ADENOSINE-5'-DIPHOSPHATE / : / ParM/StbA family protein
Function and homology information
Biological speciesBacillus thuringiensis serovar kurstaki str. YBT-1520 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsJiang, S.M. / Robinson, R.C.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Agency for Science, Technology and Research (A*STAR)12302FG012 Singapore
CitationJournal: to be published
Title: A novel plasmid-segregating actin-like protein from Bacillus thuringiensis forms dynamically unstable tubules
Authors: Jiang, S.M. / Narita, A. / Popp, D. / Ghoshdastider, U. / Lee, L.J. / Srinivasan, R. / Balasubramanian, M.K. / Oda, T. / Koh, F.J. / Larsson, M. / Robinson, R.C.
History
DepositionJan 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ParM hybrid fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3025
Polymers96,3991
Non-polymers9034
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.306, 97.275, 87.898
Angle α, β, γ (deg.)90.000, 98.820, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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Components

#1: Protein ParM hybrid fusion protein


Mass: 96398.508 Da / Num. of mol.: 1 / Mutation: F288D, M289D, P331D, M799D, F803D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar kurstaki str. YBT-1520 (bacteria)
Gene: YBT1520_33546 / Plasmid: pSY5, modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A024E1G1, UniProt: A0A0F6FJ34*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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

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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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate, pH 5.0, 5% poly-gamma-glutamic acid polymer, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2012 / Details: Quantum-315
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 15010 / % possible obs: 97.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.062 / Χ2: 0.877 / Net I/av σ(I): 15.972 / Net I/σ(I): 10.1 / Num. measured all: 46526
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.2-3.312.70.31314420.797196.1
3.31-3.4530.29915180.83398.6
3.45-3.63.10.2415160.95399
3.6-3.793.10.16815081.02598.6
3.79-4.033.20.11815181.08198.2
4.03-4.343.20.07714880.89797.6
4.34-4.783.20.06814841.04797.1
4.78-5.463.20.05615220.90797.1
5.46-6.873.10.04214860.62596.2
6.87-303.20.02115280.58396.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASER2.5.5phasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→27.75 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 1286 10.08 %Random selection
Rwork0.2289 11474 --
obs0.2349 12760 82.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.99 Å2 / Biso mean: 63.2716 Å2 / Biso min: 30.62 Å2
Refinement stepCycle: LAST / Resolution: 3.2→27.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5679 0 56 0 5735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065821
X-RAY DIFFRACTIONf_angle_d1.3077840
X-RAY DIFFRACTIONf_chiral_restr0.054875
X-RAY DIFFRACTIONf_plane_restr0.0051004
X-RAY DIFFRACTIONf_dihedral_angle_d16.5342184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.31260.3287650.285456963437
3.3126-3.46310.34011000.280886596556
3.4631-3.64530.34071340.27231196133079
3.6453-3.87310.30931630.24761424158793
3.8731-4.17120.29661590.23071450160994
4.1712-4.58930.27261650.21181479164495
4.5893-5.24950.25421640.20881474163896
5.2495-6.59910.31851650.24461487165296
6.5991-27.7510.2521710.20361530170196

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