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- PDB-4xhn: Bacillus thuringiensis ParM with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 4xhn
TitleBacillus thuringiensis ParM with AMPPNP
ComponentsUncharacterized protein
KeywordsSTRUCTURAL PROTEIN / BACTERIAL ACTIN-LIKE PROTEIN / BACTERIAL CYTOSKELETON
Function / homologyParM-like / Actin-like protein, N-terminal / Actin like proteins N terminal domain / ATPase, nucleotide binding domain / ATP binding / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / ParM/StbA family protein
Function and homology information
Biological speciesBacillus thuringiensis serovar kurstaki (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0093
Polymers47,4791
Non-polymers5312
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.443, 71.412, 114.094
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Detailsmonomer

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Components

#1: Protein Uncharacterized protein


Mass: 47478.523 Da / Num. of mol.: 1 / Mutation: M356D/F360D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar kurstaki (bacteria)
Strain: YBT-1520 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, pH 6.5, 0.2 M ammonium acetate, 25% PEG 3350

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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: Oct 10, 2008 / 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: 2.6→20 Å / Num. obs: 14466 / % possible obs: 99.4 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.039 / Χ2: 0.959 / Net I/av σ(I): 49.025 / Net I/σ(I): 19 / Num. measured all: 99481
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.646.30.3776660.898190.6
2.64-2.696.40.4216820.95998.4
2.69-2.746.70.3427130.93698.9
2.74-2.86.90.2926910.894100
2.8-2.8670.2367320.91100
2.86-2.937.10.1947020.96599.9
2.93-37.10.1897170.945100
3-3.087.10.1287140.943100
3.08-3.177.10.1037161.071100
3.17-3.2770.0887231.077100
3.27-3.397.10.0667171.048100
3.39-3.527.10.0527211.056100
3.52-3.6870.0387271.063100
3.68-3.887.10.0337240.828100
3.88-4.1270.0297390.906100
4.12-4.4370.0327230.859100
4.43-4.876.90.0367440.92100
4.87-5.576.70.0367500.91100
5.57-6.966.40.0217660.89399.7
6.96-206.50.0127991.07999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.59 Å19.88 Å
Translation2.59 Å19.88 Å

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Processing

Software
NameVersionClassification
PHASER2.3.0phasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.88 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2719 1304 10 %Random selection
Rwork0.2091 11733 --
obs0.2154 13037 89.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.52 Å2 / Biso mean: 39.4649 Å2 / Biso min: 12.4 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 32 83 2927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032888
X-RAY DIFFRACTIONf_angle_d0.8143893
X-RAY DIFFRACTIONf_chiral_restr0.029436
X-RAY DIFFRACTIONf_plane_restr0.003497
X-RAY DIFFRACTIONf_dihedral_angle_d15.1681083
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 (%)
2.6-2.69820.3389950.24183793259
2.6982-2.82070.33481120.2445993110570
2.8207-2.9690.33771280.24461201132984
2.969-3.15430.29841510.23871353150495
3.1543-3.39670.27881600.22211424158498
3.3967-3.73650.29161590.202214461605100
3.7365-4.27250.24141630.181614531616100
4.2725-5.36540.24381640.174314681632100
5.3654-19.88010.24271720.221515581730100
Refinement TLS params.Method: refined / Origin x: 74.3039 Å / Origin y: 89.8221 Å / Origin z: 122.5056 Å
111213212223313233
T0.1662 Å20.0088 Å2-0.0244 Å2-0.1209 Å2-0.0434 Å2--0.164 Å2
L2.6815 °20.0076 °2-0.3349 °2-1.4448 °2-0.319 °2--2.1097 °2
S0.0665 Å °0.0867 Å °-0.1655 Å °0.028 Å °-0.064 Å °0.1088 Å °-0.1362 Å °-0.0168 Å °0.0032 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 501
2X-RAY DIFFRACTION1allS1 - 95

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