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- PDB-3e3y: Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+ -

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Basic information

Entry
Database: PDB / ID: 3e3y
TitleQ138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+
Components
  • 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DTP*DAP*DAP*DCP*DCP*DGP*DGP*DC)-3'
  • Type-2 restriction enzyme HindII
KeywordsHYDROLASE/DNA / protein-DNA complex / endonuclease / indirect readout / 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 / Type II restriction enzyme HindII
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.13 Å
AuthorsHorton, N.C. / Babic, A.C. / Little, E.J. / Manohar, V.M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: DNA distortion and specificity in a sequence-specific endonuclease.
Authors: Babic, A.C. / Little, E.J. / Manohar, V.M. / Bitinaite, J. / Horton, N.C.
History
DepositionAug 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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
Revision 1.3Feb 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 HindII
B: Type-2 restriction enzyme HindII
E: 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DTP*DAP*DAP*DCP*DCP*DGP*DGP*DC)-3'
F: 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DTP*DAP*DAP*DCP*DCP*DGP*DGP*DC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3919
Polymers68,2424
Non-polymers1495
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-83 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.480, 91.640, 65.780
Angle α, β, γ (deg.)90.00, 104.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Type-2 restriction enzyme HindII / E.C.3.1.21.4 / R.HindII / Type II restriction enzyme HindII / Endonuclease HindII


Mass: 29839.109 Da / Num. of mol.: 2 / Mutation: Q138F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hindIIR, HI0512 / Production host: Escherichia coli (E. coli)
References: UniProt: P44413, UniProt: P17743*PLUS, type II site-specific deoxyribonuclease
#2: DNA chain 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DTP*DAP*DAP*DCP*DCP*DGP*DGP*DC)-3'


Mass: 4281.779 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, 150 mM NaCl, 10 mM HEPES pH 7.5, 5 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NaCl11
3HEPES11
4CaCl211
5H2O11
6PEG 400012
7NaCl12
8HEPES12
9CaCl212
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorDate: Jul 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 32390 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 30.67 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 5.6
Reflection shellHighest resolution: 2.13 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementResolution: 2.13→43.058 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.844 / SU ML: 0.33 / σ(F): 1.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1606 4.96 %random 5%
Rwork0.18 ---
obs0.183 32369 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.111 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 72.53 Å2 / Biso mean: 32.447 Å2 / Biso min: 14.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.522 Å20 Å2-0.679 Å2
2--2.415 Å20 Å2
3----1.893 Å2
Refinement stepCycle: LAST / Resolution: 2.13→43.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 568 5 448 4873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054594
X-RAY DIFFRACTIONf_angle_d0.9926347
X-RAY DIFFRACTIONf_chiral_restr0.06709
X-RAY DIFFRACTIONf_plane_restr0.003713
X-RAY DIFFRACTIONf_dihedral_angle_d19.6291641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.13-2.1990.2851290.2128072936100
2.199-2.2770.2981490.21527602909100
2.277-2.3680.2721550.20227702925100
2.368-2.4760.2551490.19127842933100
2.476-2.6070.2621440.18327882932100
2.607-2.770.2571350.1828352970100
2.77-2.9840.2471490.17928082957100
2.984-3.2840.2231550.16127692924100
3.284-3.7590.1931610.15327762937100
3.759-4.7350.2031280.14428422970100
4.735-43.0670.221520.2062824297699

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