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- PDB-3ebc: Structure of N141A HincII with Cognate DNA -

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Basic information

Entry
Database: PDB / ID: 3ebc
TitleStructure of N141A HincII with Cognate DNA
Components
  • 5'-D(*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DC)-3'
  • 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DCP*DGP*DAP*DCP*DGP*DGP*DGP*DC)-3'
  • Type-2 restriction enzyme HincII
KeywordsHYDROLASE/DNA / intermediate / mutant / dimerization / R-loop / Endonuclease / Hydrolase / 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, HincII / Restriction endonuclease HincII / DNA mismatch repair MutH/Restriction endonuclease, type II / DNA mismatch repair MutH/Type II restriction endonuclease superfamily / ECO RV Endonuclease; Chain A / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Type II restriction enzyme HincII
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsLittle, E.J. / Babic, A.C. / Horton, N.C.
CitationJournal: Structure / Year: 2008
Title: Early Interrogation and Recognition of DNA Sequence by Indirect Readout
Authors: Little, E.J. / Babic, A.C. / Horton, N.C.
History
DepositionAug 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type-2 restriction enzyme HincII
B: Type-2 restriction enzyme HincII
E: 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DCP*DGP*DAP*DCP*DGP*DGP*DGP*DC)-3'
F: 5'-D(*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8075
Polymers81,7534
Non-polymers551
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-76 kcal/mol
Surface area23400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.551, 91.571, 70.594
Angle α, β, γ (deg.)90.000, 107.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36593.496 Da / Num. of mol.: 2 / Mutation: N141A
Source method: isolated from a genetically manipulated source
Details: N-terminal hexaHis Tag / Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hincIIR / Plasmid: pET Blue2 / Production host: Escherichia coli (E. coli)
References: UniProt: P17743, type II site-specific deoxyribonuclease
#2: DNA chain 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DCP*DGP*DAP*DCP*DGP*DGP*DGP*DC)-3'


Mass: 4322.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HincII Cognate CG
#3: DNA chain 5'-D(*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DC)-3'


Mass: 4242.743 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HincII Cognate CG
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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

Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG 4000, 0.1M imidazole buffer, 0.2M NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2imidazole buffer11
3NaCl11
4PEG 400012
5imidazole buffer12
6NaCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2007 / Details: mirrors
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→43.56 Å / Num. all: 18533 / Num. obs: 17810 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 1.9
Reflection shellHighest resolution: 2.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 1.9 / Num. unique all: 18532 / % possible all: 96.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→43.56 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.873 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.803 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.9 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 858 4.8 %RANDOM
Rwork0.191 ---
all0.28 18533 --
obs0.195 17791 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.83 Å2 / Biso mean: 27.531 Å2 / Biso min: 6.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å2-0.58 Å2
2--0.33 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.55→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 567 1 301 4759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224613
X-RAY DIFFRACTIONr_angle_refined_deg1.382.1096366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.49225.077195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75515669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5451512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023312
X-RAY DIFFRACTIONr_nbd_refined0.2090.22415
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2327
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.217
X-RAY DIFFRACTIONr_mcbond_it0.5641.52466
X-RAY DIFFRACTIONr_mcangle_it0.98723878
X-RAY DIFFRACTIONr_scbond_it1.17832652
X-RAY DIFFRACTIONr_scangle_it1.9374.52488
LS refinement shellResolution: 2.547→2.613 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 59 -
Rwork0.293 934 -
all-993 -
obs-61124 100 %

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