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- PDB-6eg7: BbvCI B2 dimer with I3C clusters -

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Basic information

Entry
Database: PDB / ID: 6eg7
TitleBbvCI B2 dimer with I3C clusters
ComponentsBbvCI endonuclease subunit 2
KeywordsHYDROLASE / endonuclease / DNA binding protein / Type IIT restriction enzyme
Function / homologyRestriction endonuclease, type II, Bpu10I / Bpu10I restriction endonuclease / endonuclease activity / Chem-I3C / DI(HYDROXYETHYL)ETHER / BbvCI endonuclease subunit 2
Function and homology information
Biological speciesBrevibacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 3 Å
AuthorsShen, B.W. / Stoddard, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM105691 to BLS United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI.
Authors: Shen, B.W. / Doyle, L. / Bradley, P. / Heiter, D.F. / Lunnen, K.D. / Wilson, G.G. / Stoddard, B.L.
History
DepositionAug 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BbvCI endonuclease subunit 2
B: BbvCI endonuclease subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,18715
Polymers65,3182
Non-polymers4,86913
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-1 kcal/mol
Surface area29180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.888, 168.245, 106.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 7 - 281 / Label seq-ID: 7 - 281

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein BbvCI endonuclease subunit 2


Mass: 32659.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis (bacteria) / Gene: bbvCIR-2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q5D6Y4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#4: Chemical
ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H4I3NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.22 Å3/Da / Density % sol: 61.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.8 M (NH4)2SO4, 100 mM NaOAc pH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 70 / Detector: CCD / Date: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→84 Å / Num. obs: 15456 / % possible obs: 93.91 % / Observed criterion σ(I): 1 / Redundancy: 13.7 % / Biso Wilson estimate: 21.89 Å2 / CC1/2: 0.94 / Rpim(I) all: 0.035 / Rrim(I) all: 0.131 / Rsym value: 0.126 / Χ2: 1.432 / Net I/σ(I): 20.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 6 / Num. unique obs: 1124 / CC1/2: 0.964 / Rpim(I) all: 0.13 / Rrim(I) all: 0.439 / Rsym value: 0.418 / Χ2: 1.441 / % possible all: 65.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000v 714data reduction
HKL-2000v 714data scaling
SHELXDEv1phasing
RefinementMethod to determine structure: SAD / Resolution: 3→30.38 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.838 / SU B: 17.285 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26197 821 5 %RANDOM
Rwork0.21338 ---
obs0.21586 15456 93.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20 Å2
2---3.87 Å20 Å2
3---2.38 Å2
Refinement stepCycle: 1 / Resolution: 3→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4463 0 154 9 4626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124694
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.6796371
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7455553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47222.669251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.44615806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1591529
X-RAY DIFFRACTIONr_chiral_restr0.1350.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023606
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4423.6462218
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.3755.4512769
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5364.1332476
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.91165.7519221
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8361 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.997→3.074 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.63 24 -
Rwork0.342 761 -
obs--62.6 %

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