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Basic information

Entry
Database: PDB / ID: 3imb
TitleAlternative binding mode of restriction endonuclease BcnI to cognate DNA
Components
  • 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'
  • 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'
  • R.BcnI
KeywordsHYDROLASE/DNA / ENDONUCLEASE-DNA COMPLEX / RESTRICTION ENZYME / BCNI / PSEUDOPALINDROMIC SEQUENCE RECOGNITION / PSEUDOSYMMETRY / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


MvaI/BcnI restriction endonuclease, catalytic domain / MvaI/BcnI restriction endonuclease, recognition domain / MvaI/BcnI restriction endonuclease, catalytic domain / MvaI/BcnI restriction endonuclease / MvaI/BcnI restriction endonuclease, recognition domain / MvaI/BcnI restriction endonuclease family / PvuII Endonuclease; Chain A / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBrevibacillus centrosporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Szczepanowski, R.H. / Siksnys, V. / Bochtler, M.
Citation
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA
Authors: Sokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Szczepanowski, R.H. / Urbanke, C. / Siksnys, V. / Bochtler, M.
#2: Journal: Cell.Mol.Life Sci. / Year: 2007
Title: Restriction endonucleases that resemble a component of the bacterial DNA repair machinery
Authors: Sokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Siksnys, V. / Bochtler, M.
History
DepositionAug 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: R.BcnI
B: R.BcnI
C: R.BcnI
D: R.BcnI
E: 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'
F: 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'
G: 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'
H: 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'
I: 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'
J: 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'
K: 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'
L: 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)131,23712
Polymers131,23712
Non-polymers00
Water13,133729
1
A: R.BcnI
E: 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'
F: 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)32,8093
Polymers32,8093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-18 kcal/mol
Surface area11760 Å2
MethodPISA
2
B: R.BcnI
G: 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'
H: 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)32,8093
Polymers32,8093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-17 kcal/mol
Surface area12050 Å2
MethodPISA
3
C: R.BcnI
I: 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'
J: 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)32,8093
Polymers32,8093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-18 kcal/mol
Surface area11940 Å2
MethodPISA
4
D: R.BcnI
K: 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'
L: 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)32,8093
Polymers32,8093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-19 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.562, 84.053, 98.947
Angle α, β, γ (deg.)90.00, 100.09, 90.00
Int Tables number4
Space group name H-MP1211
DetailsEACH BIOLOGICAL UNIT CONTAINS ONE PROTEIN CHAIN AND TWO DNA STRANDS. THE TRIMER (ACCORDING TO PDB CONVENTIONS) IS A COMPLEX OF THE MONOMERIC RESTRICTION ENZYME WITH ITS SUBSTRATE, DOUBLE STRANDED DNA.

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Components

#1: Protein
R.BcnI


Mass: 27334.580 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus centrosporus (bacteria) / Gene: bcnIR / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267 / References: UniProt: Q8RNV8
#2: DNA chain
5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'


Mass: 2772.810 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: G STRAND
#3: DNA chain
5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'


Mass: 2701.776 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: C STRAND
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.16M Ammonium Sulfate, 0.08M Sodium Acetate trihydrate pH 4.6, 20% w/v Polyethylene Glycol 4000, 20% v/v Glycerol Anhydrous, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 8, 2006 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.89→20 Å / Num. all: 98933 / Num. obs: 98933 / % possible obs: 98.4 % / Redundancy: 2.3 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 5.4
Reflection shellResolution: 1.89→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 3.1 / Num. unique all: 14591 / Rsym value: 0.236 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2odi

2odi


Resolution: 1.89→19.81 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 0.4 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The orientation of the imidazole rings of His77 and His219 remains uncertain in all molecules in the asymmetric unit. PROGRAM CNS HAS BEEN USED FOR DNA REFINEMENT. NO SUGAR PUCKER ...Details: The orientation of the imidazole rings of His77 and His219 remains uncertain in all molecules in the asymmetric unit. PROGRAM CNS HAS BEEN USED FOR DNA REFINEMENT. NO SUGAR PUCKER CONSTRAINTS HAVE BEEN APPLIED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT HAS BEEN USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25101 4977 5 %RANDOM
Rwork0.21211 ---
obs0.21405 98906 98.19 %-
all-98906 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.39 Å2 / Biso mean: 20.1847 Å2 / Biso min: 6.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0.02 Å2
2--0.1 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.89→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7688 1452 0 729 9869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229630
X-RAY DIFFRACTIONr_bond_other_d00.026273
X-RAY DIFFRACTIONr_angle_refined_deg1.2632.16713288
X-RAY DIFFRACTIONr_angle_other_deg3.973315434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28224.59366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.634151584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1351549
X-RAY DIFFRACTIONr_chiral_restr0.0720.21482
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029554
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021695
X-RAY DIFFRACTIONr_nbd_refined0.1840.21769
X-RAY DIFFRACTIONr_nbd_other0.2470.26705
X-RAY DIFFRACTIONr_nbtor_refined0.1860.24271
X-RAY DIFFRACTIONr_nbtor_other0.1070.24227
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2723
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5791.54847
X-RAY DIFFRACTIONr_mcbond_other01.51972
X-RAY DIFFRACTIONr_mcangle_it0.97327882
X-RAY DIFFRACTIONr_scbond_it1.55834783
X-RAY DIFFRACTIONr_scangle_it2.194.55406
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 367 -
Rwork0.244 6841 -
all-7208 -
obs-6841 97.97 %
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)
10.2486-0.01570.33760.79430.13641.9639-0.01770.06030.0485-0.0683-0.0358-0.1145-0.04490.15520.0535-0.03390.02470.0128-0.02960.03320.008332.1838.20114.489
20.9077-0.388-0.11311.01830.08332.17650.018-0.10420.02720.0798-0.005-0.14270.00550.0107-0.013-0.05-0.0057-0.0306-0.04240.016-0.016523.23437.09936.718
30.33450.0270.0530.78340.01671.9092-0.01910.0254-0.0662-0.11220.02580.11350.0936-0.0812-0.0067-0.03540.0115-0.0044-0.0489-0.01570.011249.249-37.52915.123
40.7459-0.47540.36351.6857-0.35921.6322-0.0164-0.1595-0.02620.15090.10630.2223-0.0689-0.1196-0.0899-0.06050.01370.0343-0.04420.00930.0193-20.21417.87737.272
50.45360.15390.2840.9455-0.00160.94590.0169-0.07120.0250.0383-0.0497-0.03660.0439-0.04850.0328-0.02640.0366-0.0022-0.03230.0006-0.004825.315-5.16133.149
61.0736-0.358-0.14921.1224-0.09861.27510.0260.1358-0.0087-0.1123-0.03050.0303-0.0037-0.11230.0045-0.03150.0228-0.0239-0.02850.001-0.03369.28343.22318.191
70.4927-0.0409-0.04981.06830.2770.8138-0.0625-0.0962-0.00760.07450.01620.0548-0.01680.01990.0463-0.02660.0535-0.0031-0.0156-0.0016-0.023756.473-23.74533.357
81.0603-0.31080.16991.3137-0.00691.52690.06650.16290.0231-0.1901-0.0237-0.03940.03040.1027-0.0429-0.02920.00710.0142-0.03880.0098-0.0386-6.48112.15418.389
90.69890.63010.34520.7279-0.28312.3807-0.03810.14490.0027-0.0467-0.0043-0.07760.18020.00790.0424-0.03920.05850.0059-0.09680.0009-0.021427.049-5.92422.966
101.48110.33270.44960.7240.0241.83380.0512-0.11340.04260.0352-0.09750.0563-0.2194-0.1940.0463-0.05620.036-0.0097-0.0643-0.0044-0.021110.46645.17128.346
110.91210.5716-0.01470.43280.36661.8929-0.07870.079-0.001-0.02320.02670.0375-0.12590.020.0521-0.03140.053-0.0015-0.09650.0026-0.010654.512-23.21123.172
121.21240.4762-0.30190.30310.16861.70460.0351-0.02380.0704-0.0827-0.03490.06520.110.1336-0.0002-0.04710.0208-0.0081-0.07690.00190.0024-7.6359.98728.419
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 67
2X-RAY DIFFRACTION1A152 - 185
3X-RAY DIFFRACTION1A231 - 238
4X-RAY DIFFRACTION2B1 - 67
5X-RAY DIFFRACTION2B152 - 185
6X-RAY DIFFRACTION2B231 - 238
7X-RAY DIFFRACTION3C1 - 67
8X-RAY DIFFRACTION3C152 - 185
9X-RAY DIFFRACTION3C231 - 238
10X-RAY DIFFRACTION4D1 - 67
11X-RAY DIFFRACTION4D152 - 185
12X-RAY DIFFRACTION4D231 - 238
13X-RAY DIFFRACTION5A68 - 151
14X-RAY DIFFRACTION5A186 - 230
15X-RAY DIFFRACTION6B68 - 151
16X-RAY DIFFRACTION6B186 - 230
17X-RAY DIFFRACTION7C68 - 151
18X-RAY DIFFRACTION7C186 - 230
19X-RAY DIFFRACTION8D68 - 151
20X-RAY DIFFRACTION8D186 - 230
21X-RAY DIFFRACTION9E-4 - 4
22X-RAY DIFFRACTION9F-4 - 4
23X-RAY DIFFRACTION10G-4 - 4
24X-RAY DIFFRACTION10H-4 - 4
25X-RAY DIFFRACTION11I-4 - 4
26X-RAY DIFFRACTION11J-4 - 4
27X-RAY DIFFRACTION12K-4 - 4
28X-RAY DIFFRACTION12L-4 - 4

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