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- PDB-6m9g: BbvCI B2 dimer with Ta6Br14 clusters -

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Basic information

Entry
Database: PDB / ID: 6m9g
TitleBbvCI B2 dimer with Ta6Br14 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 / ACETATE ION / BROMIDE ION / HEXATANTALUM DODECABROMIDE / BbvCI endonuclease subunit 2
Function and homology information
Biological speciesBrevibacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.35 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 23, 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 1.4Jun 28, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_validate_close_contact ...database_2 / pdbx_validate_close_contact / struct_conn / 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
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,55622
Polymers65,3182
Non-polymers21,23820
Water37821
1
A: BbvCI endonuclease subunit 2
hetero molecules

B: BbvCI endonuclease subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,55622
Polymers65,3182
Non-polymers21,23820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7450 Å2
ΔGint-71 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.106, 173.304, 107.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-302-

TBR

21B-302-

TBR

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 9 - 273 / Label seq-ID: 9 - 273

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

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Components

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Protein , 1 types, 2 molecules AB

#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) / References: UniProt: Q5D6Y4

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Non-polymers , 6 types, 41 molecules

#2: Chemical
ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Br12Ta6
#3: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.8 M (NH4)2SO4, 100 mM NaOAc pH4.5 / PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.006 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 2.35→47.97 Å / Num. obs: 33287 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 21.2 % / Biso Wilson estimate: 60.63 Å2 / CC1/2: 0.887 / Rsym value: 0.16 / Net I/σ(I): 23
Reflection shellResolution: 2.35→3.43 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3011 / CC1/2: 0.877 / Rsym value: 0.703 / Χ2: 0.732 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000v7.2data reduction
HKL-2000v7.2data scaling
BUCCANEERv1.5phasing
RefinementMethod to determine structure: MIR / Resolution: 2.35→47.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.003 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23938 1699 5.1 %RANDOM
Rwork0.19766 ---
obs0.1998 31535 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.833 Å2
Baniso -1Baniso -2Baniso -3
1-10.55 Å20 Å20 Å2
2---34.17 Å20 Å2
3---23.61 Å2
Refinement stepCycle: 1 / Resolution: 2.35→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 198 21 4611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0551.9637997
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2065544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12622.874247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.92115791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8541527
X-RAY DIFFRACTIONr_chiral_restr0.1530.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023406
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_it3.1334.2262183
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.9556.3242724
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3555.0072707
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.32578.15418291
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: 8172 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.353→2.414 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 115 -
Rwork0.257 1990 -
obs--86.09 %
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)
12.14682.01470.45152.76350.14440.57720.1501-0.35610.04680.3987-0.16860.1343-0.0876-0.01110.01850.10290.00790.03210.1270.01790.016217.460349.377417.7245
22.01-1.8093-0.03153.46980.32660.2730.1550.18210.0725-0.501-0.2664-0.10240.05230.02010.11130.14030.05430.07250.02930.02950.065510.384213.057538.5979
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 283
2X-RAY DIFFRACTION2B9 - 274

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