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- PDB-1xhv: HincII bound to cleaved cognate DNA GTCGAC and Mn2+ -

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Basic information

Entry
Database: PDB / ID: 1xhv
TitleHincII bound to cleaved cognate DNA GTCGAC and Mn2+
Components
  • 5'-D(*GP*CP*CP*GP*GP*TP*C)-3'
  • 5'-D(P*GP*AP*CP*CP*GP*G)-3'
  • Type II restriction enzyme HincII
Keywordshydrolase/DNA / restriction endonuclease / phosphoryl transfer / 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
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEtzkorn, C. / Horton, N.C.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Mechanistic Insights from the Structures of HincII Bound to Cognate DNA Cleaved from Addition of Mg(2+) and Mn(2+)
Authors: Etzkorn, C. / Horton, N.C.
History
DepositionSep 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: 5'-D(*GP*CP*CP*GP*GP*TP*C)-3'
F: 5'-D(P*GP*AP*CP*CP*GP*G)-3'
G: 5'-D(*GP*CP*CP*GP*GP*TP*C)-3'
H: 5'-D(P*GP*AP*CP*CP*GP*G)-3'
I: 5'-D(*GP*CP*CP*GP*GP*TP*C)-3'
J: 5'-D(P*GP*AP*CP*CP*GP*G)-3'
K: 5'-D(*GP*CP*CP*GP*GP*TP*C)-3'
L: 5'-D(P*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)136,28334
Polymers135,07512
Non-polymers1,20922
Water18,5011027
1
E: 5'-D(*GP*CP*CP*GP*GP*TP*C)-3'
F: 5'-D(P*GP*AP*CP*CP*GP*G)-3'
G: 5'-D(*GP*CP*CP*GP*GP*TP*C)-3'
H: 5'-D(P*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)68,14217
Polymers67,5376
Non-polymers60411
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: 5'-D(*GP*CP*CP*GP*GP*TP*C)-3'
J: 5'-D(P*GP*AP*CP*CP*GP*G)-3'
K: 5'-D(*GP*CP*CP*GP*GP*TP*C)-3'
L: 5'-D(P*GP*AP*CP*CP*GP*G)-3'
C: Type II restriction enzyme HincII
D: Type II restriction enzyme HincII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,14217
Polymers67,5376
Non-polymers60411
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.8, 178.2, 257.3
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-1312-

HOH

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Components

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


Mass: 2114.398 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: phosphoramidite synthetic chemistry
#2: DNA chain
5'-D(P*GP*AP*CP*CP*GP*G)-3'


Mass: 1834.230 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: phosphoramidite synthetic chemistry
#3: Protein
Type II restriction enzyme HincII / Endonuclease HincII / R.HincII


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


Mass: 54.938 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1027 / 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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, NaCl, citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NaCl11
3citrate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 53281 / % possible obs: 89.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 16.2

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Processing

Software
NameClassification
MADNESSdata collection
HKL-2000data reduction
CNSrefinement
MADNESSdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KC6 without solvent

1kc6


Resolution: 2.5→50 Å / Cross valid method: R free / σ(F): 2 / Stereochemistry target values: as in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2664 -5% random
Rwork0.199 ---
obs-53281 89.3 %-
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8085 1064 22 1027 10198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.36

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