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- PDB-3v1z: Crystal structure of Type IIF restriction endonuclease Bse634I wi... -

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Basic information

Entry
Database: PDB / ID: 3v1z
TitleCrystal structure of Type IIF restriction endonuclease Bse634I with cognate DNA
Components
  • DNA (5'-D(*TP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP*G)-3')
  • Endonuclease Bse634IR
KeywordsHydrolase/DNA / RESTRICTION ENDONUCLEASE / protein-DNA complex / HYDROLASE / Hydrolase-DNA complex
Function / homology
Function and homology information


endonuclease activity / metal ion binding
Similarity search - Function
Restriction Endonuclease - #10 / Restriction endonuclease, type II, Cfr10I/Bse634I / Cfr10I/Bse634I restriction endonuclease / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Endonuclease Bse634IR
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.2 Å
AuthorsManakova, E.N. / Grazulis, S. / Golovenko, D. / Tamulaitiene, G.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease.
Authors: Manakova, E. / Grazulis, S. / Zaremba, M. / Tamulaitiene, G. / Golovenko, D. / Siksnys, V.
History
DepositionDec 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease Bse634IR
B: Endonuclease Bse634IR
C: DNA (5'-D(*TP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP*G)-3')
D: DNA (5'-D(*TP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)75,4654
Polymers75,4654
Non-polymers00
Water3,927218
1
A: Endonuclease Bse634IR
C: DNA (5'-D(*TP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP*G)-3')

A: Endonuclease Bse634IR
C: DNA (5'-D(*TP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)75,4654
Polymers75,4654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9620 Å2
ΔGint-56 kcal/mol
Surface area27220 Å2
MethodPISA
2
B: Endonuclease Bse634IR
D: DNA (5'-D(*TP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP*G)-3')

B: Endonuclease Bse634IR
D: DNA (5'-D(*TP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)75,4654
Polymers75,4654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9900 Å2
ΔGint-53 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.008, 83.632, 123.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Endonuclease Bse634IR


Mass: 33762.758 Da / Num. of mol.: 2 / Mutation: R226A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: 1422 / Gene: bse634IR / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267
References: UniProt: Q8RT53, type II site-specific deoxyribonuclease
#2: DNA chain DNA (5'-D(*TP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP*G)-3')


Mass: 3969.561 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE RESIDUES AT POSITION 110, 111, AND 130 ARE CORRECTLY IDENTIFIED AND THE ...AUTHORS STATE THAT THE RESIDUES AT POSITION 110, 111, AND 130 ARE CORRECTLY IDENTIFIED AND THE BIOCHEMICAL DATA SHOWS THAT THE PROTEIN IS ACTIVE.

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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: 2.4 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 293 K / pH: 5.5
Details: 100mM Na-acetate pH 4.25-5.5, 10mM CaCl2 or CaAc2, 4-8% (w/v) of PEG8000, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→69.14 Å / Num. obs: 33372 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 39.35 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 16.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.307 / % possible all: 95.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
SCALA3.1.20data scaling
PDB_EXTRACT3.006data extraction
MOLREPphasing
RefinementStarting model: PDB ENTRY 1KNV

1knv


Resolution: 2.2→62.14 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.142 / SU ML: 0.198 / SU R Cruickshank DPI: 0.366 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.283 3719 10.1 %RANDOM
Rwork0.226 ---
obs0.232 33238 95.9 %-
all-38563 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2--3.75 Å20 Å2
3----2.41 Å2
Refinement stepCycle: LAST / Resolution: 2.2→62.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4695 526 0 218 5439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225448
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0092.0857482
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2675591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74925228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78815929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1811524
X-RAY DIFFRACTIONr_chiral_restr0.0650.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213876
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_it0.3291.52936
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.60424790
X-RAY DIFFRACTIONr_scbond_it0.72132512
X-RAY DIFFRACTIONr_scangle_it1.1564.52692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 187 -
Rwork0.268 1814 -
obs--71.01 %
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)
10.7687-0.04240.12060.48570.00821.3062-0.0154-0.07480.05690.06720.0069-0.1119-0.08460.09440.00850.0151-0.0052-0.01440.0161-0.00760.054114.89045.524360.1388
20.61610.00060.04940.49550.08291.12640.02840.07820.1129-0.2238-0.060.0041-0.23410.00090.03160.15180.04710.00840.03830.02250.04690.044815.84954.1074
31.28520.1782-0.73451.3118-0.14070.838-0.0475-0.1311-0.04330.00330.0379-0.04270.0432-0.10130.00960.0090.002-0.00870.0910.00410.0166-0.67760.855670.2701
41.1632-0.32880.64560.66550.57551.42970.10820.10930.0751-0.2071-0.1273-0.0348-0.0685-0.00110.01910.20060.1090.0180.08610.01910.00731.0546-0.0851-6.1284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 292
2X-RAY DIFFRACTION1A301 - 422
3X-RAY DIFFRACTION2B4 - 292
4X-RAY DIFFRACTION2B301 - 361
5X-RAY DIFFRACTION3C1 - 13
6X-RAY DIFFRACTION3C101 - 120
7X-RAY DIFFRACTION4D1 - 13
8X-RAY DIFFRACTION4D101 - 113

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