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- PDB-9ez7: BsmI (Nicking top mutant) crystallized with Ca2+ and cognate dsDNA -

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Basic information

Entry
Database: PDB / ID: 9ez7
TitleBsmI (Nicking top mutant) crystallized with Ca2+ 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: 2.031 Å
AuthorsSieskind, R. / Missoury, S. / Madru, C. / Commenge, I. / Niogret, G. / Hollenstein, M. / 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 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)85,7587
Polymers85,4483
Non-polymers3114
Water8,575476
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, Analytical Ultra-Centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-46 kcal/mol
Surface area30530 Å2
Unit cell
Length a, b, c (Å)98.55, 132.989, 63.285
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: 77504.422 Da / Num. of mol.: 1 / Mutation: E109V
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 , 4 types, 480 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, pH 6.5 100 mM CaCl2 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: 2.031→79.179 Å / Num. obs: 39820 / % possible obs: 93.1 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.297 / Net I/σ(I): 7.9
Reflection shellResolution: 2.031→2.2 Å / Rmerge(I) obs: 2.389 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 39820 / % possible all: 69.5

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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: 2.031→29.45 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.302 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.333 / SU Rfree Blow DPI: 0.214 / SU Rfree Cruickshank DPI: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 1880 -RANDOM
Rwork0.1988 ---
obs0.2004 39796 73.1 %-
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.3041 Å20 Å20 Å2
2---1.1419 Å20 Å2
3---4.446 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.031→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5417 527 15 476 6435
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086145HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.938417HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2081SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes963HARMONIC5
X-RAY DIFFRACTIONt_it6145HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion801SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4609SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion17.89
LS refinement shellResolution: 2.031→2.13 Å
RfactorNum. reflection% reflection
Rfree0.3481 34 -
Rwork0.264 --
obs--11.02 %
Refinement TLS params.Origin x: 16.5873 Å / Origin y: -22.8905 Å / Origin z: -10.5936 Å
111213212223313233
T-0.0704 Å2-0.002 Å2-0.0132 Å2--0.0428 Å2-0.0095 Å2--0.0544 Å2
L0.1757 °20.0897 °2-0.105 °2-0.1695 °2-0.0921 °2--0.1412 °2
S0.011 Å °0.0082 Å °-0.0069 Å °0.0082 Å °-0.0064 Å °-0.0022 Å °-0.0069 Å °-0.0022 Å °-0.0045 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A1 - 676
2X-RAY DIFFRACTION1{ *|* }A701 - 704
3X-RAY DIFFRACTION1{ *|* }A801 - 1223
4X-RAY DIFFRACTION1{ *|* }B1
5X-RAY DIFFRACTION1{ *|* }E1 - 13
6X-RAY DIFFRACTION1{ *|* }E101 - 128
7X-RAY DIFFRACTION1{ *|* }F1 - 13
8X-RAY DIFFRACTION1{ *|* }F101 - 126

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