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- PDB-2p14: Crystal structure of small subunit (R.BspD6I2) of the heterodimer... -

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Basic information

Entry
Database: PDB / ID: 2p14
TitleCrystal structure of small subunit (R.BspD6I2) of the heterodimeric restriction endonuclease R.BspD6I
ComponentsHeterodimeric restriction endonuclease R.BspD6I small subunit
KeywordsHYDROLASE / heterodimeric restriction endonuclease
Function / homologyRestriction Endonuclease - #50 / Restriction endonuclease, type II, AlwI / AlwI restriction endonuclease / Restriction Endonuclease / endonuclease activity / 3-Layer(aba) Sandwich / Alpha Beta / Heterodimeric restriction endonuclease R.BspD6I small subunit
Function and homology information
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKachalova, G.S. / Bartunik, H.D. / Artyukh, R.I. / Rogulin, E.A. / Yunusova, A.K. / Zheleznaya, L.A. / Matvienko, N.I.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural analysis of the heterodimeric type IIS restriction endonuclease R.BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit.
Authors: Kachalova, G.S. / Rogulin, E.A. / Yunusova, A.K. / Artyukh, R.I. / Perevyazova, T.A. / Matvienko, N.I. / Zheleznaya, L.A. / Bartunik, H.D.
History
DepositionMar 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterodimeric restriction endonuclease R.BspD6I small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7934
Polymers22,5091
Non-polymers2843
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.429, 38.360, 61.995
Angle α, β, γ (deg.)90.000, 101.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heterodimeric restriction endonuclease R.BspD6I small subunit


Mass: 22508.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: D6 / Gene: bspD6IR2 / Plasmid: pET28c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A3FEV8, type II site-specific deoxyribonuclease
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 1.99 Å3/Da / Density % sol: 38.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 2.0 M (NH4)2SO4, 0.2 M Li2SO4, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 17, 2006 / Details: AU-COATED PLANAR and TOROIDAL MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 29298 / Num. obs: 28430 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 2.91 % / Biso Wilson estimate: 18.66 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.87 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.24 / Num. unique all: 1428

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
Bestdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ewf

2ewf


Resolution: 1.5→10.75 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.399 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1428 5 %RANDOM
Rwork0.177 ---
obs0.179 28355 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.891 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0.36 Å2
2---0.89 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.5→10.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1533 0 16 159 1708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221655
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9852257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6945209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51525.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07815306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.856154
X-RAY DIFFRACTIONr_chiral_restr0.0970.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021271
X-RAY DIFFRACTIONr_nbd_refined0.2080.2810
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21161
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.222
X-RAY DIFFRACTIONr_mcbond_it0.9861.5992
X-RAY DIFFRACTIONr_mcangle_it1.54121582
X-RAY DIFFRACTIONr_scbond_it2.5793746
X-RAY DIFFRACTIONr_scangle_it4.0034.5664
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 115 -
Rwork0.255 1976 -
obs-2091 99.67 %

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