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- PDB-1kc6: HincII Bound to Cognate DNA -

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Basic information

Entry
Database: PDB / ID: 1kc6
TitleHincII Bound to Cognate DNA
Components
  • 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
  • TYPE II RESTRICTION ENZYME HINCII
KeywordsHYDROLASE/DNA / restriction endonuclease / blunt cutting / protein-dna / indirect readout / dna bending / 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 / MAD / Resolution: 2.6 Å
AuthorsHorton, N.C. / Dorner, L.F. / Perona, J.J.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation.
Authors: Horton, N.C. / Dorner, L.F. / Perona, J.J.
History
DepositionNov 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2001Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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.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
Remark 999sequence The authors maintain that residues THR 130 and TRP 173 are correct.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
F: 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
G: 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
H: 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
A: TYPE II RESTRICTION ENZYME HINCII
B: TYPE II RESTRICTION ENZYME HINCII
C: TYPE II RESTRICTION ENZYME HINCII
D: TYPE II RESTRICTION ENZYME HINCII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,98410
Polymers133,9388
Non-polymers462
Water9,350519
1
E: 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
F: 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
A: TYPE II RESTRICTION ENZYME HINCII
B: TYPE II RESTRICTION ENZYME HINCII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0156
Polymers66,9694
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
H: 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
C: TYPE II RESTRICTION ENZYME HINCII
D: TYPE II RESTRICTION ENZYME HINCII


Theoretical massNumber of molelcules
Total (without water)66,9694
Polymers66,9694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.120, 177.670, 256.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: DNA chain
5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'


Mass: 3664.380 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
TYPE II RESTRICTION ENZYME HINCII / ENDONUCLEASE HINCII


Mass: 29820.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P17743, type II site-specific deoxyribonuclease
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.78 Å3/Da / Density % sol: 57.3 %
Crystal growpH: 5.5
Details: 0.1M sodium citrate, 0.15M NaCl, 20% PEG 4K, pH 5.5
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium citrate11
2NaClSodium chloride11
3PEG 4K11
Crystal grow
*PLUS
Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: Horton, N.C., (1999) Acta Crystallogr., D55, 1943.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.2 mg/mlHincII-DNA complex1drop
220 %PEG40001reservoir
30.1 Msodium citrate1reservoirpH5.5
40.12 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 42701 / % possible obs: 87.3 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 16.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.191 / % possible all: 76
Reflection
*PLUS
Highest resolution: 2.56 Å / Lowest resolution: 20 Å / Num. measured all: 91893
Reflection shell
*PLUS
% possible obs: 76 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Cross valid method: free R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2071 4.3 %random
Rwork0.219 ---
obs-41613 87.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.403 Å20 Å20 Å2
2---0.537 Å20 Å2
3----2.866 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7626 984 2 519 9131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.088
X-RAY DIFFRACTIONc_mcbond_it1.245
X-RAY DIFFRACTIONc_mcangle_it2.104
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.747
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3892 171 3.6 %
Rwork0.2965 3405 -
obs--75.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.parmprotein.top
X-RAY DIFFRACTION2dna-rna_rep.parmdna-rna.top
X-RAY DIFFRACTION3water_rep.parmwater.top
X-RAY DIFFRACTION4ion.parmion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. reflection obs: 34951 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.284 / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.088
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Rfactor Rfree: 0.384 / % reflection Rfree: 3.6 % / Rfactor obs: 0.286

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