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- PDB-9f38: BsmI (wild-type) crystallized with Ca2+ and cognate dsDNA -

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Basic information

Entry
Database: PDB / ID: 9f38
TitleBsmI (wild-type) crystallized with Ca2+ and cognate dsDNA
Components
  • BsmI
  • DNA (Bottom strand)
  • 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: 2.85 Å
AuthorsSieskind, R. / Missoury, S. / Madru, C. / Commenge, I. / Niogret, G. / Hollenstein, M. / Rondelez, Y. / Haouz, A. / Sauguet, L. / Legrand, P. / 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 25, 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)
U: DNA (Top strand)
V: DNA (Bottom strand)
Z: BsmI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,79814
Polymers172,3276
Non-polymers4718
Water3,135174
1
A: BsmI
E: DNA (Bottom strand)
F: DNA (Top strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2846
Polymers86,1633
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-80 kcal/mol
Surface area28490 Å2
2
U: DNA (Top strand)
V: DNA (Bottom strand)
Z: BsmI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5148
Polymers86,1633
Non-polymers3515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-73 kcal/mol
Surface area28590 Å2
Unit cell
Length a, b, c (Å)65.735, 129.885, 100.733
Angle α, β, γ (deg.)90, 95.5, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AZ

#1: Protein BsmI


Mass: 78220.250 Da / Num. of mol.: 2
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, 4 molecules EVFU

#2: DNA chain DNA (Bottom strand)


Mass: 3893.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)
#3: DNA chain DNA (Top strand)


Mass: 4049.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)

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Non-polymers , 4 types, 182 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES, pH 6.5 100 mM CaCl2 25 % PEG 400 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: 2.85→48.7 Å / Num. obs: 24310 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.957 / Rmerge(I) obs: 0.345 / Net I/σ(I): 4.5
Reflection shellResolution: 2.85→2.92 Å / Rmerge(I) obs: 1.292 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 24310 / CC1/2: 0.531

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→48.7 Å / Cor.coef. Fo:Fc: 0.802 / Cor.coef. Fo:Fc free: 0.759 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.672
RfactorNum. reflection% reflectionSelection details
Rfree0.2934 1187 -RANDOM
Rwork0.2744 ---
obs0.2753 24310 61.8 %-
Displacement parametersBiso mean: 47.58 Å2
Baniso -1Baniso -2Baniso -3
1-9.396 Å20 Å29.1031 Å2
2--0.3208 Å20 Å2
3----9.7168 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: LAST / Resolution: 2.85→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11042 1054 19 174 12289
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00512505HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.817125HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4281SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1972HARMONIC5
X-RAY DIFFRACTIONt_it12492HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1612SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8748SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion18.52
LS refinement shellResolution: 2.85→2.93 Å
RfactorNum. reflection% reflection
Rfree0.3729 26 -
Rwork0.3176 --
obs0.3208 487 15.9 %
Refinement TLS params.Origin x: 7.3266 Å / Origin y: -21.486 Å / Origin z: 26.0662 Å
111213212223313233
T0.1881 Å2-0.0492 Å20.1933 Å2--0.1374 Å2-0.018 Å2---0.208 Å2
L0.0237 °2-0.027 °2-0.1488 °2-0.2909 °2-0.2489 °2--0.541 °2
S-0.0274 Å °-0.0143 Å °-0.0245 Å °-0.0143 Å °-0.0062 Å °0.1173 Å °-0.0245 Å °0.1173 Å °0.0336 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A1 - 676
2X-RAY DIFFRACTION1{ *|* }E1 - 13
3X-RAY DIFFRACTION1{ *|* }F1 - 13
4X-RAY DIFFRACTION1{ *|* }M1 - 3
5X-RAY DIFFRACTION1{ *|* }N1 - 3
6X-RAY DIFFRACTION1{ *|* }O1
7X-RAY DIFFRACTION1{ *|* }U1 - 13
8X-RAY DIFFRACTION1{ *|* }V1 - 13
9X-RAY DIFFRACTION1{ *|* }W1 - 177
10X-RAY DIFFRACTION1{ *|* }X1
11X-RAY DIFFRACTION1{ *|* }Z1 - 676

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