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- PDB-2e52: Crystal structural analysis of HindIII restriction endonuclease i... -

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Basic information

Entry
Database: PDB / ID: 2.0E+52
TitleCrystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA at 2.0 angstrom resolution
Components
  • DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')
  • Type II restriction enzyme HindIII
Keywordshydrolase/DNA / Type II restriction enzyme HindIII(E.C.3.1.21.4)/DNA / hydrolase-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system
Similarity search - Function
Type II restriction endonuclease, HindIII / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1510 / Restriction endonuclease, type II, HindIII / Restriction endonuclease, type II, HindIII superfamily / HindIII restriction endonuclease / Restriction Endonuclease / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DNA / DNA (> 10) / Type II restriction enzyme HindIII
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWatanabe, N. / Sato, C. / Tanaka, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations
Authors: Watanabe, N. / Takasaki, Y. / Sato, C. / Ando, S. / Tanaka, I.
History
DepositionDec 18, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Remark 650HELIX Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type II restriction enzyme HindIII
C: Type II restriction enzyme HindIII
B: Type II restriction enzyme HindIII
D: Type II restriction enzyme HindIII
E: DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')
F: DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')
G: DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')
H: DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')
I: DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')
J: DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,51917
Polymers161,97310
Non-polymers5467
Water17,439968
1
A: Type II restriction enzyme HindIII
B: Type II restriction enzyme HindIII
E: DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')
G: DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5667
Polymers77,3234
Non-polymers2433
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13680 Å2
ΔGint-95 kcal/mol
Surface area26100 Å2
MethodPISA
2
C: Type II restriction enzyme HindIII
D: Type II restriction enzyme HindIII
F: DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')
H: DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6258
Polymers77,3234
Non-polymers3024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13750 Å2
ΔGint-87 kcal/mol
Surface area26060 Å2
MethodPISA
3
I: DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')
J: DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-10 kcal/mol
Surface area4570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.125, 131.532, 93.718
Angle α, β, γ (deg.)90.00, 111.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Type II restriction enzyme HindIII / Endonuclease HindIII / R.HindIII


Mass: 34998.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: Rd KW20 / Gene: hindIIIR / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)plysS
References: UniProt: P43870, type II site-specific deoxyribonuclease
#2: DNA chain
DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3')


Mass: 3663.392 Da / Num. of mol.: 6 / Source method: obtained synthetically
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 968 / 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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 3350, 0.08M Ammonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2Ammonium Acetate11
3HOH11
4PEG 335012
5Ammonium Acetate12
6HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.684 Å / Num. all: 126130 / Num. obs: 126130 / % possible obs: 100 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 7.7 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 29.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 11.8 / Num. unique all: 12567 / Rsym value: 0.156 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→39.684 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / Rfactor Rfree error: 6327 / SU B: 2.872 / SU ML: 0.084 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21665 6327 5 %RANDOM
Rwork0.17467 ---
obs0.17672 119772 99.88 %-
all-119772 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.59 Å2
2--0.14 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→39.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9826 1458 36 968 12288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211655
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5032.13315971
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82751190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79925.656488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93152008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2941540
X-RAY DIFFRACTIONr_chiral_restr0.1110.21788
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028088
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.25417
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.28039
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.21071
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9521.56227
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50829666
X-RAY DIFFRACTIONr_scbond_it2.22736726
X-RAY DIFFRACTIONr_scangle_it3.3644.56305
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 469 -
Rwork0.18 --
obs-8710 98.86 %

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