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- PDB-3hqg: Crystal structure of restriction endonuclease EcoRII catalytic C-... -

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Basic information

Entry
Database: PDB / ID: 3hqg
TitleCrystal structure of restriction endonuclease EcoRII catalytic C-terminal domain in complex with cognate DNA
Components
  • 5'-D(*TP*AP*GP*CP*CP*TP*GP*GP*TP*CP*GP*A)-3'
  • 5'-D(*TP*CP*GP*AP*CP*CP*AP*GP*GP*CP*TP*A)-3'
  • Type-2 restriction enzyme EcoRII
KeywordsHYDROLASE/DNA / restriction endonuclease / EcoRII / nucleotide flipping / protein-DNA complex / DNA recognition / Endonuclease / Hydrolase / Magnesium / Nuclease / Restriction system / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding
Similarity search - Function
Restriction endonuclease, type II, EcoRII, N-terminal / Restriction endonuclease EcoRII, N-terminal / Restriction Endonuclease - #80 / Restriction endonuclease, type II, EcoRII, C-terminal / EcoRII, C-terminal domain superfamily / EcoRII C terminal / DNA-binding pseudobarrel domain superfamily / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Type II restriction enzyme EcoRII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsGolovenko, D. / Manakova, E. / Grazulis, S. / Tamulaitiene, G. / Siksnys, V.
Citation
Journal: Nucleic Acids Res. / Year: 2009
Title: Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.
Authors: Golovenko, D. / Manakova, E. / Tamulaitiene, G. / Grazulis, S. / Siksnys, V.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of type iie restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold
Authors: Zhou, X.E. / Wang, Y. / Reuter, M. / Mucke, M. / Kruger, D.H. / Meehan, E.J. / Chen, L.
History
DepositionJun 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
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_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: Type-2 restriction enzyme EcoRII
B: 5'-D(*TP*CP*GP*AP*CP*CP*AP*GP*GP*CP*TP*A)-3'
C: 5'-D(*TP*AP*GP*CP*CP*TP*GP*GP*TP*CP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9954
Polymers32,9033
Non-polymers921
Water1,20767
1
A: Type-2 restriction enzyme EcoRII
B: 5'-D(*TP*CP*GP*AP*CP*CP*AP*GP*GP*CP*TP*A)-3'
C: 5'-D(*TP*AP*GP*CP*CP*TP*GP*GP*TP*CP*GP*A)-3'
hetero molecules

A: Type-2 restriction enzyme EcoRII
B: 5'-D(*TP*CP*GP*AP*CP*CP*AP*GP*GP*CP*TP*A)-3'
C: 5'-D(*TP*AP*GP*CP*CP*TP*GP*GP*TP*CP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9908
Polymers65,8066
Non-polymers1842
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)77.054, 57.971, 61.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe second part of the biological assembly is generated by the two fold axis: -x+1, -y, z.

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Components

#1: Protein Type-2 restriction enzyme EcoRII / R.EcoRII / Type II restriction enzyme EcoRII / Endonuclease EcoRII


Mass: 25577.191 Da / Num. of mol.: 1
Fragment: C-terminal catalytic domain (UNP residues 183-404)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECORII, ecoRIIR / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109
References: UniProt: P14633, type II site-specific deoxyribonuclease
#2: DNA chain 5'-D(*TP*CP*GP*AP*CP*CP*AP*GP*GP*CP*TP*A)-3'


Mass: 3647.393 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*AP*GP*CP*CP*TP*GP*GP*TP*CP*GP*A)-3'


Mass: 3678.403 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 26% PEG1500, 25% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.808 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2006
RadiationMonochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.808 Å / Relative weight: 1
ReflectionResolution: 2.11→47.836 Å / Num. obs: 8835 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 12.41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.74120.332.31499212540.3399.8
2.74-2.9111.90.2173.51429612050.21799.7
2.91-3.1111.90.1335.61339011230.13399.9
3.11-3.3611.90.0789.21248510530.07899.9
3.36-3.6811.80.05313.2114399720.05399.8
3.68-4.1111.70.03817.6105028950.03899.8
4.11-4.7511.60.0319.391547890.03100
4.75-5.8111.40.02822.576866770.02899.9
5.81-8.2211.10.02623.260715460.02699.8
8.22-47.849.70.02818.431143210.02898

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.465 / Cor.coef. Fo:Fc: 0.409 / Cor.coef. Io to Ic: 0.411
Highest resolutionLowest resolution
Rotation4 Å12 Å
Translation4 Å12 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
AMoREphasing
MOSFLMdata reduction
SCALA3.2.19data scaling
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NA6

1na6


Resolution: 2.6→47.84 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.875 / WRfactor Rfree: 0.29 / WRfactor Rwork: 0.223 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.766 / SU B: 35.862 / SU ML: 0.346 / SU R Cruickshank DPI: 0.365 / SU Rfree: 0.43 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.293 834 9.5 %RANDOM
Rwork0.236 7976 --
obs0.242 8810 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 90.36 Å2 / Biso mean: 45.712 Å2 / Biso min: 5.97 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2---2.88 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 486 6 67 2365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212594
X-RAY DIFFRACTIONr_angle_refined_deg1.0122.223352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.755223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71423.19194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6415326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0241516
X-RAY DIFFRACTIONr_chiral_restr0.0640.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211666
X-RAY DIFFRACTIONr_mcbond_it0.2861.51111
X-RAY DIFFRACTIONr_mcangle_it0.55121793
X-RAY DIFFRACTIONr_scbond_it0.52231483
X-RAY DIFFRACTIONr_scangle_it0.934.51558
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.552 60 -
Rwork0.366 580 -
all-640 -
obs--99.22 %
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)
11.28940.3072-0.49231.0715-0.3111.19910.00670.1765-0.02160.02380.03220.1258-0.0233-0.0557-0.03890.12860.0053-0.06320.0313-0.00180.095524.3881-6.3289-14.6345
20.99051.78690.85053.23831.54440.7942-0.09860.06040.1275-0.21430.07750.2269-0.13940.05190.02120.1840.03740.02530.12490.01380.140737.55140.0438-19.7907
38.14820.9261-3.68974.12530.43171.8514-0.2870.395-0.19310.23510.1650.2820.1803-0.14330.1220.19290.051-0.03580.0725-0.01020.052639.4921-2.1521-19.5849
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A183 - 404
2X-RAY DIFFRACTION1A1
3X-RAY DIFFRACTION1A2 - 405
4X-RAY DIFFRACTION2B-6 - 5
5X-RAY DIFFRACTION2B9 - 52
6X-RAY DIFFRACTION3C-5 - 6
7X-RAY DIFFRACTION3C39 - 63

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