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- PDB-2odh: Restriction Endonuclease BCNI in the Absence of DNA -

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Basic information

Entry
Database: PDB / ID: 2odh
TitleRestriction Endonuclease BCNI in the Absence of DNA
ComponentsR.BcnI
KeywordsHYDROLASE / MONOMERIC ENDONUCLEASE / RESTRICTION ENZYME / BCNI
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
ACETATE ION / DI(HYDROXYETHYL)ETHER / R.BcnI
Similarity search - Component
Biological speciesBrevibacillus centrosporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsSokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Szczepanowski, R.H. / Urbanke, K. / 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 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Dec 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: R.BcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5003
Polymers27,3351
Non-polymers1652
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.176, 68.176, 127.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein R.BcnI


Mass: 27334.580 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17 M ammonium acetate, 0.085 M tri-sodium citrate pH 5.6, 25.5% PEG 4000, 15% glycerol, 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: May 20, 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: 1.6→30 Å / Num. all: 40038 / Num. obs: 40038 / % possible obs: 99.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 26.3 Å2 / Rsym value: 0.07 / Net I/σ(I): 4
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 5737 / Rsym value: 0.25 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SHELXDphasing
SHARPphasing
NCSREFmodel building
REFMAC5.1.24refinement
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MLPHAREphasing
DMphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.6→29.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.56 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS REFINEMENT USED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2018 5.1 %RANDOM
Rwork0.203 ---
all0.204 39959 --
obs0.204 39959 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.393 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 11 205 2100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211960
X-RAY DIFFRACTIONr_bond_other_d0.0060.021802
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9662646
X-RAY DIFFRACTIONr_angle_other_deg0.78534199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7395243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022183
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02388
X-RAY DIFFRACTIONr_nbd_refined0.2130.2375
X-RAY DIFFRACTIONr_nbd_other0.2520.22090
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.21170
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8591.51194
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5421930
X-RAY DIFFRACTIONr_scbond_it2.1093766
X-RAY DIFFRACTIONr_scangle_it3.3434.5716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.214 166
Rwork0.21 2729
obs-2729
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)
11.8112-0.12090.34040.5791-0.18960.9584-0.06010.07270.11420.01560.01010.016-0.0506-0.05560.050.1007-0.0158-0.02910.14740.04250.08182.18117.74354.949
21.4223-0.98570.58282.7276-2.12432.1412-0.03280.46130.2614-0.0659-0.2062-0.26590.01660.12240.2390.0377-0.0139-0.02480.26560.12750.079.84825.14534.282
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 691 - 69
2X-RAY DIFFRACTION1AA156 - 182156 - 182
3X-RAY DIFFRACTION1AA233 - 238233 - 238
4X-RAY DIFFRACTION2AA70 - 15570 - 155
5X-RAY DIFFRACTION2AA183 - 232183 - 232

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