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- PDB-6maf: native BbvCI A2B2 tetramer at low resolution -

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Basic information

Entry
Database: PDB / ID: 6maf
Titlenative BbvCI A2B2 tetramer at low resolution
Components
  • BbvCI endonuclease subunit 1
  • BbvCI endonuclease subunit 2
KeywordsHYDROLASE / endonuclease / DNA binding protein / Type IIT restriction enzyme
Function / homologyRestriction endonuclease, type II, Bpu10I / Bpu10I restriction endonuclease / endonuclease activity / BbvCI endonuclease subunit 2 / BbvCI endonuclease subunit 1
Function and homology information
Biological speciesBrevibacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.79 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 27, 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 1.3Sep 18, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rrim_I_all
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: BbvCI endonuclease subunit 1
B: BbvCI endonuclease subunit 1
C: BbvCI endonuclease subunit 2
D: BbvCI endonuclease subunit 2


Theoretical massNumber of molelcules
Total (without water)128,2764
Polymers128,2764
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.152, 113.152, 115.001
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHETYRTYRBB6 - 2646 - 264
21PHEPHETYRTYRAA6 - 2646 - 264
12ASNASNPHEPHECC6 - 2826 - 282
22ASNASNPHEPHEDD6 - 2826 - 282

NCS ensembles :
ID
1
2

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Components

#1: Protein BbvCI endonuclease subunit 1


Mass: 31478.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis (bacteria) / Gene: bbvCIR-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5D6Y5
#2: 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) / References: UniProt: Q5D6Y4

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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: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 15% PEF4k, 0.2M Ammonium Sulfate, Citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 1, 2016
RadiationMonochromator: yale mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.79→28.4 Å / Num. obs: 15368 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 137.6 Å2 / CC1/2: 0.784 / Rpim(I) all: 0.104 / Rrim(I) all: 0.1045 / Rsym value: 0.129 / Χ2: 1.009 / Net I/σ(I): 11.4
Reflection shellResolution: 3.792→3.889 Å / Redundancy: 5 % / Num. unique obs: 1117 / Rsym value: 1.47 / % possible all: 93.93

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000V7.2data reduction
HKL-2000V7.2data scaling
PHASERV2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EG7

6eg7


Resolution: 3.79→28.4 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.82 / SU B: 73.611 / SU ML: 1.08 / Cross valid method: THROUGHOUT / ESU R Free: 1.125
RfactorNum. reflection% reflectionSelection details
Rfree0.38792 768 4.8 %RANDOM
Rwork0.2973 ---
obs0.30167 15368 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 177.963 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å2-1.91 Å20 Å2
2---3.82 Å20 Å2
3---12.38 Å2
Refinement stepCycle: 1 / Resolution: 3.79→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8630 0 0 0 8630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198804
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.95711876
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86451060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.21924.286434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.19151588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7511556
X-RAY DIFFRACTIONr_chiral_restr0.1130.21298
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216644
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B166220.02
12A166220.02
21C183300.01
22D183300.01
LS refinement shellResolution: 3.792→3.889 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 66 -
Rwork0.522 1064 -
obs--93.93 %

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