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- PDB-4xho: Bacillus thuringiensis ParM with ATP -

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Basic information

Entry
Database: PDB / ID: 4xho
TitleBacillus thuringiensis ParM with ATP
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 / ADENOSINE-5'-TRIPHOSPHATE / : / ParM/StbA family protein
Function and homology information
Biological speciesBacillus thuringiensis serovar kurstaki (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)48,0103
Polymers47,4791
Non-polymers5312
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.830, 73.156, 113.726
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-618-

HOH

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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
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: 2.65→30 Å / Num. obs: 14327 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.057 / Χ2: 0.972 / Net I/av σ(I): 30.962 / Net I/σ(I): 15.4 / Num. measured all: 102248
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.65-2.77.20.4956941.0111100
2.7-2.747.30.4056950.915100
2.74-2.87.30.3527150.881100
2.8-2.857.30.2736980.932100
2.85-2.927.30.2186890.953100
2.92-2.987.30.1997230.94899.9
2.98-3.067.30.1666980.947100
3.06-3.147.30.1257000.946100
3.14-3.237.30.16990.941100
3.23-3.347.20.0887330.916100
3.34-3.467.30.0746900.949100
3.46-3.67.20.0637070.894100
3.6-3.767.20.0577240.959100
3.76-3.967.20.0527080.869100
3.96-4.27.10.0557191.178100
4.2-4.5370.0557191.164100
4.53-4.9870.0637241.567100
4.98-5.76.90.0567451.174100
5.7-7.166.60.0377490.68299.9
7.16-306.40.0317980.60499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.63 Å28.83 Å
Translation2.63 Å28.83 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: 2.65→28.825 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2712 1368 10.05 %Random selection
Rwork0.203 12245 --
obs0.2099 13613 94.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.05 Å2 / Biso mean: 36.5238 Å2 / Biso min: 7.45 Å2
Refinement stepCycle: LAST / Resolution: 2.65→28.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 32 132 3061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112973
X-RAY DIFFRACTIONf_angle_d1.5874007
X-RAY DIFFRACTIONf_chiral_restr0.089445
X-RAY DIFFRACTIONf_plane_restr0.008515
X-RAY DIFFRACTIONf_dihedral_angle_d17.0681121
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6281-2.7220.3538950.242584493966
2.722-2.83090.30831270.25151115124288
2.8309-2.95960.33311380.24171236137496
2.9596-3.11540.31781380.23511239137797
3.1154-3.31040.33531420.22581268141098
3.3104-3.56550.26981400.21211276141699
3.5655-3.92360.28121420.19251260140299
3.9236-4.48950.23571400.15941286142698
4.4895-5.64930.20351490.164813371486100
5.6493-28.82680.24611570.20871384154199
Refinement TLS params.Method: refined / Origin x: -47.1379 Å / Origin y: -55.4987 Å / Origin z: 235.4359 Å
111213212223313233
T0.1307 Å20.0245 Å20.082 Å2--0.0449 Å20.114 Å2--0.0784 Å2
L2.8707 °2-0.0149 °20.016 °2-2.4338 °21.4053 °2--3.3461 °2
S0.0977 Å °-0.1111 Å °0.2182 Å °-0.0925 Å °-0.0662 Å °-0.1659 Å °0.114 Å °-0.104 Å °0.0049 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 501
2X-RAY DIFFRACTION1allS1 - 135

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