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- PDB-2q10: RESTRICTION ENDONUCLEASE BcnI (WILD TYPE)-COGNATE DNA SUBSTRATE C... -

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Basic information

Entry
Database: PDB / ID: 2q10
TitleRESTRICTION ENDONUCLEASE BcnI (WILD TYPE)-COGNATE DNA SUBSTRATE COMPLEX
Components
  • DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3')
  • DNA (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 / MOLECULAR REPLACEMENT / Resolution: 1.75 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: 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
DepositionMay 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 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 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_asym_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.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3')
D: DNA (5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3')
E: DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3')
F: DNA (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)68,27711
Polymers68,0866
Non-polymers1915
Water11,620645
1
C: DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3')
D: DNA (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)34,1596
Polymers34,0433
Non-polymers1163
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3')
F: DNA (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)34,1195
Polymers34,0433
Non-polymers762
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.354, 87.551, 79.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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DNA chain , 2 types, 4 molecules CEDF

#1: DNA chain DNA (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 DNA (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: 27334.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus centrosporus (bacteria) / Gene: bcnIR / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267 / References: UniProt: Q8RNV8

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Non-polymers , 3 types, 650 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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.05 Å3/Da / Density % sol: 40.07 %
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, 30% (V/V) 2-METHYL-2,4-PENTANEDIOL , pH 4.60, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1CALCIUM CHLORIDE DIHYDRATE11
2SODIUM ACETATE TRIHYDRATE11
32-METHYL-2,4-PENTANEDIOL11
4CALCIUM CHLORIDE DIHYDRATE12
5SODIUM ACETATE TRIHYDRATE12
62-METHYL-2,4-PENTANEDIOL12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
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: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 57635 / Num. obs: 57635 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 5.8
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 8336 / Rsym value: 0.26 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2ODI

2odi


Resolution: 1.75→29.72 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.451 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS REFINEMENT HAVE BEEN USED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2882 5 %RANDOM
Rwork0.174 ---
all0.176 57579 --
obs0.176 57579 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.68 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 890 5 645 5384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225175
X-RAY DIFFRACTIONr_bond_other_d0.0070.023330
X-RAY DIFFRACTIONr_angle_refined_deg1.352.1937173
X-RAY DIFFRACTIONr_angle_other_deg0.91138206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94924.66191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79615830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3471526
X-RAY DIFFRACTIONr_chiral_restr0.0770.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025094
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02898
X-RAY DIFFRACTIONr_nbd_refined0.1990.2891
X-RAY DIFFRACTIONr_nbd_other0.2090.23576
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22221
X-RAY DIFFRACTIONr_nbtor_other0.0790.22350
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2531
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1510.213
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7991.52656
X-RAY DIFFRACTIONr_mcbond_other0.1661.51029
X-RAY DIFFRACTIONr_mcangle_it1.03224134
X-RAY DIFFRACTIONr_scbond_it1.833206
X-RAY DIFFRACTIONr_scangle_it2.2374.53039
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 204 -
Rwork0.229 4004 -
obs-4004 100 %
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)
10.8372-0.0446-0.17341.9141-0.20110.66010.02670.0260.02540.0653-0.01510.0062-0.101-0.0226-0.0116-0.04680.003-0.0039-0.0386-0.00240.00748.71826.39747.642
20.4679-0.2670.00910.53550.09730.8476-0.0528-0.06070.0377-0.01370.0236-0.1026-0.01990.24110.0292-0.0529-0.0084-0.0070.03810.01150.014469.92513.85949.636
31.2302-0.2925-0.17071.40130.14370.5426-0.0332-0.12150.05370.08280.05540.0268-0.0679-0.0458-0.0222-0.05240.0187-0.0093-0.0308-0.0033-0.00949.36225.77989.547
40.83760.010.18050.66250.07720.3235-0.0317-0.071-0.0101-0.00160.0276-0.1197-0.01940.03780.0041-0.0509-0.0035-0.0043-0.0468-0.00280.015470.46213.6688.97
51.28350.15270.20370.6858-0.01131.1066-0.00320.034-0.0035-0.04340.0819-0.01020.04790.0461-0.0787-0.04470.01040.0038-0.02-0.01380.006659.57712.11846.629
61.1242-0.13210.61450.4209-0.0821.17680.0061-0.004-0.0462-0.02220.07070.0035-0.0035-0.0209-0.0768-0.04290.00660.003-0.054-0.01460.015659.88611.95286.812
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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