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- PDB-4xe7: Bacillus thuringiensis ParM in apo form -

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Basic information

Entry
Database: PDB / ID: 4xe7
TitleBacillus thuringiensis ParM in apo form
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 / : / ParM/StbA family protein
Function and homology information
Biological speciesBacillus thuringiensis serovar kurstaki (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 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
DepositionDec 23, 2014Deposition 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 / diffrn_radiation_wavelength / 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

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)47,5271
Polymers47,5271
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.248, 116.430, 52.171
Angle α, β, γ (deg.)90.000, 115.730, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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Components

#1: Protein Uncharacterized protein


Mass: 47526.719 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium citrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2008 / Details: Quantum-315
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33791 / % possible obs: 94.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.096 / Χ2: 4.441 / Net I/av σ(I): 27.414 / Net I/σ(I): 12.8 / Num. measured all: 136335
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.033.70.31713280.641174.7
2.03-2.073.80.27916000.85990.2
2.07-2.113.90.24616800.81595
2.11-2.1540.2216830.82293.9
2.15-2.240.19816810.91995.6
2.2-2.2540.17716731.01293.3
2.25-2.3140.16316711.0495.6
2.31-2.3740.1516781.25893
2.37-2.443.90.13616821.38594.7
2.44-2.5240.12816621.7194.1
2.52-2.6140.12416871.97993.2
2.61-2.7140.11617202.37996.7
2.71-2.8440.11117353.12997.6
2.84-2.994.10.10517403.97198.1
2.99-3.174.20.09817595.12498.3
3.17-3.424.20.0917607.14898.7
3.42-3.764.20.08317668.28598.4
3.76-4.314.20.079173410.18397.2
4.31-5.434.20.077175911.34597.4
5.43-504.20.09179318.67398

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å35.29 Å
Translation2.5 Å35.29 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
PHASER2.3.0phasing
PDB_EXTRACT3.11data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→25.319 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 3902 5.97 %Random selection
Rwork0.1856 61460 --
obs0.1885 65362 92.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.73 Å2 / Biso mean: 37.608 Å2 / Biso min: 12.82 Å2
Refinement stepCycle: LAST / Resolution: 2→25.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 0 330 3639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083363
X-RAY DIFFRACTIONf_angle_d1.1474526
X-RAY DIFFRACTIONf_chiral_restr0.045500
X-RAY DIFFRACTIONf_plane_restr0.005590
X-RAY DIFFRACTIONf_dihedral_angle_d15.7491282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02210.3101870.24321383147060
2.0221-2.04760.27811350.2361823195877
2.0476-2.07460.26481410.22912189233092
2.0746-2.1030.24661240.22592189231392
2.103-2.1330.31821380.22582194233291
2.133-2.16480.28741290.21942201233092
2.1648-2.19860.26441490.21512138228793
2.1986-2.23470.26811250.21092233235891
2.2347-2.27320.2771420.21442132227492
2.2732-2.31450.28821310.20872185231692
2.3145-2.3590.25261330.20762198233190
2.359-2.40710.23231450.20672164230992
2.4071-2.45940.27421390.19772144228389
2.4594-2.51650.26391300.19312164229493
2.5165-2.57940.24411420.2012187232991
2.5794-2.64910.29951370.19322180231793
2.6491-2.72690.22111650.20352268243394
2.7269-2.81480.25191390.19042216235597
2.8148-2.91530.2261430.19562318246196
2.9153-3.03190.23461510.19192352250399
3.0319-3.16960.24471540.1932346250098
3.1696-3.33640.23041440.18522316246098
3.3364-3.54490.23461510.18312347249898
3.5449-3.81770.25781530.17392305245898
3.8177-4.20030.21271360.1632307244397
4.2003-4.80450.19331540.14352301245597
4.8045-6.03960.19261360.16572316245297
6.0396-25.32110.17381490.16872364251399
Refinement TLS params.Method: refined / Origin x: -16.3737 Å / Origin y: -17.0246 Å / Origin z: -5.6562 Å
111213212223313233
T0.1631 Å20.0047 Å2-0.0024 Å2-0.1619 Å20.0236 Å2--0.1655 Å2
L0.267 °2-0.1685 °2-0.0807 °2-0.4488 °20.2558 °2--0.4331 °2
S-0.0102 Å °-0.0073 Å °-0.0451 Å °-0.0303 Å °-0.0046 Å °0.0396 Å °0.0378 Å °0.0085 Å °0.0101 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 419
2X-RAY DIFFRACTION1allS1 - 330

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