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- PDB-3e44: Q138F HincII bound to cleaved DNA (GTT | AAC) and Mn2+ -

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Basic information

Entry
Database: PDB / ID: 3.0E+44
TitleQ138F HincII bound to cleaved DNA (GTT | AAC) and Mn2+
Components
  • 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DT)-3'
  • 5'-D(P*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 / Type II restriction enzyme HincII / Type II restriction enzyme HindII
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.52 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 / struct_conn ...database_2 / 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 / _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

Downloads & links

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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*DT)-3'
F: 5'-D(P*DAP*DAP*DCP*DCP*DGP*DGP*DC)-3'
G: 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DT)-3'
H: 5'-D(P*DAP*DAP*DCP*DCP*DGP*DGP*DC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,37210
Polymers68,1526
Non-polymers2204
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-113 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.694, 91.788, 66.180
Angle α, β, γ (deg.)90.00, 105.30, 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*DT)-3'


Mass: 2129.409 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*DAP*DAP*DCP*DCP*DGP*DGP*DC)-3'


Mass: 2107.413 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, 150 mM NaCl, 10 mM HEPES pH 7.5, 2.5 mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NaCl11
3HEPES11
4MnCl211
5PEG 400012
6NaCl12
7HEPES12
8MnCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.913321 Å
DetectorDate: Apr 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.913321 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 23041 / Num. obs: 22903 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 39.71 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.8
Reflection shellResolution: 2.522→2.59 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementResolution: 2.52→63.834 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.799 / SU ML: 0.36 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.257 956 4.84 %random 5%
Rwork0.18 ---
obs0.184 19750 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.514 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso max: 80.45 Å2 / Biso mean: 39.092 Å2 / Biso min: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.75 Å20 Å21.084 Å2
2--1.464 Å20 Å2
3---4.286 Å2
Refinement stepCycle: LAST / Resolution: 2.52→63.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 570 4 292 4783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084643
X-RAY DIFFRACTIONf_angle_d1.2076407
X-RAY DIFFRACTIONf_chiral_restr0.071712
X-RAY DIFFRACTIONf_plane_restr0.005722
X-RAY DIFFRACTIONf_dihedral_angle_d20.6911670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.52-2.6530.3261390.21926662805100
2.653-2.8190.3211260.19926952821100
2.819-3.0370.2781450.1826582803100
3.037-3.3420.2261230.15327002823100
3.342-3.8260.2571270.1472681280899
3.826-4.820.2131540.1412680283499
4.82-63.8550.251420.1972714285699

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