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- PDB-9ez5: BsmI (Inactive) crystallized with Mg2+ and cognate dsDNA -

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Basic information

Entry
Database: PDB / ID: 9ez5
TitleBsmI (Inactive) crystallized with Mg2+ and cognate dsDNA
Components
  • BsmI
  • DNA (Bottom strand)
  • DNA (Top strand)
KeywordsHYDROLASE / Restriction endonuclease / DNA cleavage
Function / homologymetal ion binding / DNA / DNA (> 10) / BsmI
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.846 Å
AuthorsSieskind, R. / Missoury, S. / Madru, C. / Commenge, I. / Niogret, G. / Rondelez, Y. / Haouz, A. / Legrand, P. / Sauguet, L. / Delarue, M.
Funding support France, 1items
OrganizationGrant numberCountry
Not funded France
CitationJournal: Commun Biol / Year: 2025
Title: Crystal structures of monomeric BsmI restriction endonuclease reveal coordinated sequential cleavage of two DNA strands.
Authors: Sieskind, R. / Missoury, S. / Madru, C. / Commenge, I. / Niogret, G. / Hollenstein, M. / Rondelez, Y. / Sauguet, L. / Haouz, A. / Legrand, P. / Delarue, M.
History
DepositionApr 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BsmI
E: DNA (Bottom strand)
F: DNA (Top strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1485
Polymers85,9173
Non-polymers2312
Water7,909439
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, Analytical Ultra-Centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-30 kcal/mol
Surface area30460 Å2
Unit cell
Length a, b, c (Å)98.481, 132.584, 63.745
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BsmI


Mass: 77974.078 Da / Num. of mol.: 1 / Mutation: E109V, R507D, G509V, E546V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: bsmIR / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RLN4

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DNA chain , 2 types, 2 molecules EF

#2: DNA chain DNA (Bottom strand)


Mass: 3893.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)
#3: DNA chain DNA (Top strand)


Mass: 4049.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)

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Non-polymers , 3 types, 441 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 49.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100mM MES, pH6.5 200mM MgCl2 30% PEG400 25% Guanidine HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.846→79.058 Å / Num. obs: 38714 / % possible obs: 92.1 % / Redundancy: 14.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.05 / Rrim(I) all: 0.193 / Net I/σ(I): 9.6
Reflection shellResolution: 1.846→2.023 Å / Redundancy: 13.7 % / Rmerge(I) obs: 2.061 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1936 / CC1/2: 0.626 / Rpim(I) all: 0.559 / Rrim(I) all: 2.138 / % possible all: 51.1

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.846→34.08 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.882 / SU R Cruickshank DPI: 0.331 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.36 / SU Rfree Blow DPI: 0.231 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 1871 -RANDOM
Rwork0.2065 ---
obs0.2085 38701 53.4 %-
Displacement parametersBiso mean: 30.25 Å2
Baniso -1Baniso -2Baniso -3
1--10.8406 Å20 Å20 Å2
2---8.145 Å20 Å2
3---18.9856 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.846→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5458 527 13 439 6437
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096194HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.958482HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2103SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes971HARMONIC5
X-RAY DIFFRACTIONt_it6194HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion806SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5077SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion17.63
LS refinement shellResolution: 1.85→1.97 Å
RfactorNum. reflection% reflection
Rfree0.2613 27 -
Rwork0.2708 --
obs0.2704 775 6.07 %
Refinement TLS params.Origin x: 16.5217 Å / Origin y: 22.6365 Å / Origin z: 10.5178 Å
111213212223313233
T-0.1873 Å20.0054 Å20.0002 Å2--0.1402 Å2-0.0593 Å2--0.2561 Å2
L0.1994 °2-0.1597 °20.0398 °2-0.1701 °2-0.1716 °2--0.1439 °2
S0.0054 Å °-0.0234 Å °0.0354 Å °-0.0234 Å °0.0141 Å °-0.004 Å °0.0354 Å °-0.004 Å °-0.0195 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A1 - 676
2X-RAY DIFFRACTION1{ *|* }C1
3X-RAY DIFFRACTION1{ *|* }E1 - 13
4X-RAY DIFFRACTION1{ *|* }F1 - 13
5X-RAY DIFFRACTION1{ *|* }L1
6X-RAY DIFFRACTION1{ *|* }W1 - 439

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