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- PDB-9ezd: BsmI (Bottom Nicking mutant) crystallized with Mg2+ and cognate d... -

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Basic information

Entry
Database: PDB / ID: 9ezd
TitleBsmI (Bottom Nicking mutant) crystallized with Mg2+ and cognate dsDNA (Post-reactive complex)
Components
  • (DNA (Bottom strand - ...) x 2
  • BsmI
  • DNA (Top strand)
KeywordsHYDROLASE / Restriction endonuclease / DNA cleavage
Function / homologyDNA / DNA (> 10) / BsmI
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.635 Å
AuthorsSieskind, R. / Missoury, S. / Madru, C. / Commenge, I. / Niogret, G. / Rondelez, Y. / Haouz, A. / Legrand, P. / Sauguet, L. / Delarue, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
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 11, 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 - 5'-part)
F: DNA (Top strand)
G: DNA (Bottom strand - 3'-part)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3437
Polymers86,0884
Non-polymers2553
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Analyticial Ultra-centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.213, 130.419, 62.542
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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DNA (Bottom strand - ... , 2 types, 2 molecules EG

#2: DNA chain DNA (Bottom strand - 5'-part)


Mass: 2337.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)
#4: DNA chain DNA (Bottom strand - 3'-part)


Mass: 1511.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)

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Protein / DNA chain , 2 types, 2 molecules AF

#1: Protein BsmI


Mass: 78190.234 Da / Num. of mol.: 1 / Mutation: 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
#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 , 4 types, 54 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES pH6.5 100 mM MgCl2 25% PEG400 35% 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: 0.97856 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: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.635→78.455 Å / Num. obs: 12735 / % possible obs: 91.1 % / Redundancy: 11.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.52 / Rpim(I) all: 0.162 / Rrim(I) all: 0.546 / Net I/σ(I): 5.5
Reflection shellResolution: 2.635→2.957 Å / Redundancy: 9.7 % / Rmerge(I) obs: 2.439 / Num. unique obs: 637 / CC1/2: 0.433 / Rpim(I) all: 0.82 / Rrim(I) all: 2.577 / % possible all: 65.7

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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: 2.635→78.45 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.857 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.557
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 653 -RANDOM
Rwork0.2188 ---
obs0.2205 12735 52.1 %-
Displacement parametersBiso mean: 41.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.4282 Å20 Å20 Å2
2---1.7398 Å20 Å2
3---0.3116 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.635→78.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5422 526 14 51 6013
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076145HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.878408HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2098SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes965HARMONIC5
X-RAY DIFFRACTIONt_it6145HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion798SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4502SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion19.14
LS refinement shellResolution: 2.635→2.89 Å
RfactorNum. reflection% reflection
Rfree0.3107 26 -
Rwork0.2961 --
obs--6.94 %
Refinement TLS params.Origin x: 16.3696 Å / Origin y: 22.2859 Å / Origin z: 10.5333 Å
111213212223313233
T-0.0676 Å2-0.0157 Å20.0301 Å2--0.1185 Å20.0045 Å2--0.0997 Å2
L0.2134 °2-0.0951 °20.2187 °2-0.4664 °2-0.1969 °2--0.2851 °2
S0.0335 Å °-0.0289 Å °0.0494 Å °-0.0289 Å °-0.0239 Å °0.0351 Å °0.0494 Å °0.0351 Å °-0.0095 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A1 - 676
2X-RAY DIFFRACTION1{ *|* }B1
3X-RAY DIFFRACTION1{ *|* }C1
4X-RAY DIFFRACTION1{ *|* }E1 - 8
5X-RAY DIFFRACTION1{ *|* }F1 - 13
6X-RAY DIFFRACTION1{ *|* }G1 - 5
7X-RAY DIFFRACTION1{ *|* }L1
8X-RAY DIFFRACTION1{ *|* }W1 - 51

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