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- PDB-2odi: Restriction Endonuclease BCNI-Cognate DNA Substrate Complex -

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Basic information

Entry
Database: PDB / ID: 2odi
TitleRestriction Endonuclease BCNI-Cognate DNA Substrate Complex
Components
  • 5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3'
  • 5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3'
  • R.BcnI
KeywordsHydrolase/DNA / ENDONUCLEASE-DNA COMPLEX / RESTRICTION ENZYME / BCNI / 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
DNA / DNA (> 10) / R.BcnI
Similarity search - Component
Biological speciesBrevibacillus centrosporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsSokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Szczepanowski, R.H. / Urbanke, C. / Siksnys, V. / Bochtler, M.
Citation
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.
#1: Journal: To be Published
Title: Structural and Mechanistic Similarities between Restriction Endonucleases BcnI and MvaI and the DNA Repair Protein MutH.
Authors: Sokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Siksnys, V. / Bochtler, M.
History
DepositionDec 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
C: 5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3'
D: 5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3'
E: 5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3'
F: 5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3'
A: R.BcnI
B: R.BcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,84011
Polymers68,6496
Non-polymers1915
Water11,710650
1
C: 5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3'
D: 5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3'
A: R.BcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4406
Polymers34,3243
Non-polymers1163
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3'
F: 5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3'
B: R.BcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4005
Polymers34,3243
Non-polymers762
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.553, 87.870, 79.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-854-

HOH

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Components

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DNA chain , 2 types, 4 molecules CEDF

#1: DNA chain 5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3'


Mass: 3352.214 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3'


Mass: 3356.182 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#3: Protein R.BcnI


Mass: 27615.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus centrosporus (bacteria) / Gene: bcnIR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RNV8

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Non-polymers , 3 types, 655 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.02 M calcium chloride dihydrate, 0.1 M sodium acetate trihydrate pH 4.6 and 30% (v/v) 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1calcium chloride dihydrate11
2sodium acetate trihydrate11
32-methyl-2,4-pentanediol11
4H2O11
5calcium chloride dihydrate12
6sodium acetate trihydrate12
72-methyl-2,4-pentanediol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.97955 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 4, 2006 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97955 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 99034 / Num. obs: 99034 / % possible obs: 97.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.05 / Net I/σ(I): 8.5
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 14110 / Rsym value: 0.25 / % possible all: 96.3

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Processing

Software
NameVersionClassification
SHELXDphasing
SHARPphasing
NCSREFmodel building
REFMAC5.2.0019refinement
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXEmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.45→28.38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.063 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS REFINEMENT HAVE BEEN USED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 4977 5 %RANDOM
Rwork0.174 ---
all0.175 98979 --
obs0.175 98979 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.875 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 890 5 650 5389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225115
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1922.1977092
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59624.624186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93715822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2981525
X-RAY DIFFRACTIONr_chiral_restr0.0740.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023523
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.22221
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23383
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2585
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.140.213
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9711.52581
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03424073
X-RAY DIFFRACTIONr_scbond_it1.62833169
X-RAY DIFFRACTIONr_scangle_it2.2224.53019
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.257 370
Rwork0.204 6749
obs-6749
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)
10.76990.0981-0.16271.268-0.13160.42380.03040.01140.01370.0318-0.00650.0381-0.0585-0.0279-0.0239-0.04120.0028-0.002-0.01530.001-0.010348.71826.39747.642
20.4282-0.04920.01850.49590.04320.4208-0.0266-0.04710.0040.0001-0.0014-0.0780.00120.10.028-0.0425-0.0012-0.00550.01720.007-0.010269.92513.85949.636
31.0791-0.3296-0.22011.080.220.3964-0.0069-0.08520.05680.05290.03460.0396-0.0459-0.0272-0.0277-0.03440.0117-0.0031-0.0158-0.002-0.022349.36225.77989.547
40.77690.01670.12030.59880.04280.324-0.0256-0.07910.00050.00460.012-0.09450.00240.05650.0135-0.03770.0012-0.0002-0.0057-0.0038-0.006170.46213.6688.97
51.10370.07020.20110.6757-0.08760.74860.01030.0354-0.0117-0.03990.0610.01110.0390.0182-0.0713-0.03780.0070.0028-0.0133-0.0078-0.023859.57712.11846.629
60.8846-0.15110.38230.5581-0.26451.15460.0135-0.0025-0.0544-0.01480.05420.0115-0.0011-0.0037-0.0677-0.03430.00630.0049-0.0308-0.0013-0.013959.88611.95286.812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AE1 - 691 - 69
2X-RAY DIFFRACTION1AE156 - 182156 - 182
3X-RAY DIFFRACTION1AE233 - 238233 - 238
4X-RAY DIFFRACTION2AE70 - 15570 - 155
5X-RAY DIFFRACTION2AE183 - 232183 - 232
6X-RAY DIFFRACTION3BF1 - 691 - 69
7X-RAY DIFFRACTION3BF156 - 182156 - 182
8X-RAY DIFFRACTION3BF233 - 238233 - 238
9X-RAY DIFFRACTION4BF70 - 15570 - 155
10X-RAY DIFFRACTION4BF183 - 232183 - 232
11X-RAY DIFFRACTION5CA-4 - 61 - 11
12X-RAY DIFFRACTION5DB-4 - 61 - 11
13X-RAY DIFFRACTION6EC-4 - 61 - 11
14X-RAY DIFFRACTION6FD-4 - 61 - 11

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