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- PDB-6mag: native BbvCI B2 dimer in space group C222 -

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Basic information

Entry
Database: PDB / ID: 6mag
Titlenative BbvCI B2 dimer in space group C222
ComponentsBbvCI endonuclease subunit 2
KeywordsHYDROLASE / endonuclease / DNA binding protein / Type IIT restriction enzyme
Function / homologyRestriction endonuclease, type II, Bpu10I / Bpu10I restriction endonuclease / endonuclease activity / ACETATE ION / PHOSPHATE ION / BbvCI endonuclease subunit 2
Function and homology information
Biological speciesBrevibacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)100,34729
Polymers97,9773
Non-polymers2,37026
Water6,810378
1
A: BbvCI endonuclease subunit 2
hetero molecules

A: BbvCI endonuclease subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,73118
Polymers65,3182
Non-polymers1,41316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6670 Å2
ΔGint-44 kcal/mol
Surface area27760 Å2
MethodPISA
2
B: BbvCI endonuclease subunit 2
hetero molecules

B: BbvCI endonuclease subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,16622
Polymers65,3182
Non-polymers1,84820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z1
Buried area7440 Å2
ΔGint-49 kcal/mol
Surface area27900 Å2
MethodPISA
3
C: BbvCI endonuclease subunit 2
hetero molecules

C: BbvCI endonuclease subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,79818
Polymers65,3182
Non-polymers1,47916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z1
Buried area6960 Å2
ΔGint-39 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.712, 165.707, 141.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-431-

HOH

21A-508-

HOH

31A-526-

HOH

41A-529-

HOH

51B-419-

HOH

61B-495-

HOH

71B-504-

HOH

81C-442-

HOH

91C-483-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 285
2010B3 - 285
1020A3 - 285
2020C3 - 285
1030B3 - 285
2030C3 - 285

NCS ensembles :
ID
1
2
3

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Components

#1: Protein BbvCI endonuclease subunit 2


Mass: 32659.137 Da / Num. of mol.: 3
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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.4 M (NH4)H2PO4 / PH range: 4.0-5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Apr 9, 2009
RadiationMonochromator: crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→28.65 Å / Num. obs: 62192 / % possible obs: 96.3 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 44.29 Å2 / Rpim(I) all: 0.056 / Rrim(I) all: 0.112 / Rsym value: 0.107 / Χ2: 0.913 / Net I/σ(I): 10.8
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 3.7 % / Num. unique obs: 6515 / CC1/2: 0.548 / Rpim(I) all: 0.523 / Rrim(I) all: 1.071 / Rsym value: 0.925 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000v7.2data reduction
HKL-2000v7.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EG7

6eg7


Resolution: 2.07→28.65 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.739 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24321 3219 4.9 %RANDOM
Rwork0.19566 ---
obs0.19801 62192 95.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.297 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å20 Å20 Å2
2--0.91 Å20 Å2
3---1.31 Å2
Refinement stepCycle: 1 / Resolution: 2.07→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6822 0 151 378 7351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127413
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.65510045
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8945904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31923.043414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.059151283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.411545
X-RAY DIFFRACTIONr_chiral_restr0.130.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025672
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_it1.9042.2793545
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3353.3894469
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1832.6473868
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.71931.76610983
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)
11A94700.07
12B94700.07
21A95010.07
22C95010.07
31B93620.08
32C93620.08
LS refinement shellResolution: 2.074→2.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 260 -
Rwork0.32 4389 -
obs--93.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.47322.1896-0.82221.9539-0.70920.34070.1215-0.1769-0.09330.1531-0.1698-0.0786-0.08750.0360.04830.3912-0.024-0.02570.02440.00080.0088-63.752-16.179460.3647
20.2434-0.8636-0.22123.46590.77480.2703-0.0928-0.049-0.03020.22120.04910.13940.0730.07890.04370.23950.10150.01040.17010.02290.0139-30.0852-19.706613.2971
33.56140.94650.78530.25540.20550.1798-0.08320.30050.1332-0.02870.05140.03490.01620.09610.03180.22790.0880.01630.23980.01870.0066-45.9048-47.07433.715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 284
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B3 - 284
4X-RAY DIFFRACTION3C3 - 284

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