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Basic information

Entry
Database: PDB / ID: 3a4k
TitleCrystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 angstrom resolution
Components
  • DNA (5'-D(*GP*CP*CP*A)-3')
  • DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
  • DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3')
  • Type-2 restriction enzyme HindIII
KeywordsHYDROLASE/DNA / Type II restriction enzyme HindIII(E.C.3.1.21.4)/DNA / hydrolase-DNA COMPLEX / Endonuclease / Hydrolase / Nuclease / Restriction system
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 / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsWatanabe, N. / Sato, C. / Takasaki, Y. / 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
DepositionJul 9, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _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-2 restriction enzyme HindIII
C: Type-2 restriction enzyme HindIII
B: Type-2 restriction enzyme HindIII
D: Type-2 restriction enzyme HindIII
E: DNA (5'-D(*GP*CP*CP*A)-3')
F: DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3')
G: DNA (5'-D(*GP*CP*CP*A)-3')
H: DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3')
I: DNA (5'-D(*GP*CP*CP*A)-3')
J: DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3')
K: DNA (5'-D(*GP*CP*CP*A)-3')
L: DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3')
M: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
N: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,08328
Polymers162,34614
Non-polymers73714
Water10,323573
1
A: Type-2 restriction enzyme HindIII
B: Type-2 restriction enzyme HindIII
E: DNA (5'-D(*GP*CP*CP*A)-3')
F: DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3')
I: DNA (5'-D(*GP*CP*CP*A)-3')
J: DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,87813
Polymers77,5106
Non-polymers3697
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14170 Å2
ΔGint-88 kcal/mol
Surface area26020 Å2
MethodPISA
2
C: Type-2 restriction enzyme HindIII
D: Type-2 restriction enzyme HindIII
G: DNA (5'-D(*GP*CP*CP*A)-3')
H: DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3')
K: DNA (5'-D(*GP*CP*CP*A)-3')
L: DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,87813
Polymers77,5106
Non-polymers3697
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14180 Å2
ΔGint-85 kcal/mol
Surface area25910 Å2
MethodPISA
3
M: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
N: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-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 area4460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.460, 132.211, 94.070
Angle α, β, γ (deg.)90.000, 111.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ACBD

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


Mass: 35136.320 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

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DNA chain , 3 types, 10 molecules EGIKFHJLMN

#2: DNA chain
DNA (5'-D(*GP*CP*CP*A)-3')


Mass: 1175.819 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: 5'-fragment of cleaved cognate DNA with HindIIIR
#3: DNA chain
DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3')


Mass: 2442.616 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: 3'-fragment of cleaved cognate DNA with HindIIIR
#4: DNA chain DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This DNA sequence synthesized chemically contains cognate HindIIIR recognition sequence and elongated scaffolds on both sides

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Non-polymers , 5 types, 587 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsMG ION WAS USED IN THE EXPERIMENT, BUT METAL IONS AT SITES O, P, Q AND R IN THE STRUCTURE HAVE BEEN ...MG ION WAS USED IN THE EXPERIMENT, BUT METAL IONS AT SITES O, P, Q AND R IN THE STRUCTURE HAVE BEEN DEDUCED AS MN ION USING REFINED TEMPERATURE FACTORS.

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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: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3350, ammonium acetate, Magnesium ion, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 20, 2006 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 100664 / % possible obs: 99.8 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 24.7
Reflection shellResolution: 2.17→2.23 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.5 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0062refinement
PDB_EXTRACT3.005data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E52

2e52


Resolution: 2.17→41.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.791 / SU ML: 0.125 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 5018 5 %RANDOM
Rwork0.178 ---
obs0.18 100399 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.53 Å2 / Biso mean: 36.106 Å2 / Biso min: 15.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.53 Å2
2--0.51 Å20 Å2
3----0.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.2388 Å / Luzzati sigma a obs: 0.192792 Å
Refinement stepCycle: LAST / Resolution: 2.17→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9775 1462 36 573 11846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02211594
X-RAY DIFFRACTIONr_angle_refined_deg1.7792.13315887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21551182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.52225.753485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57151991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5671537
X-RAY DIFFRACTIONr_chiral_restr0.120.21783
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028057
X-RAY DIFFRACTIONr_mcbond_it0.9691.55954
X-RAY DIFFRACTIONr_mcangle_it1.82929619
X-RAY DIFFRACTIONr_scbond_it2.80435640
X-RAY DIFFRACTIONr_scangle_it4.2874.56268
LS refinement shellResolution: 2.169→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 374 -
Rwork0.225 6827 -
all-7201 -
obs--97.32 %

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