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- PDB-1tx3: HINCII BOUND TO COGNATE DNA -

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Basic information

Entry
Database: PDB / ID: 1tx3
TitleHINCII BOUND TO COGNATE DNA
Components
  • 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
  • Type II restriction enzyme HindII
KeywordsHYDROLASE/DNA / RESTRICTION ENDONUCLEASE / BLUNT CUTTING / PROTEIN-DNA / INDIRECT READOUT / DNA BENDING / 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 / SAD / Resolution: 2.5 Å
AuthorsHorton, N.C. / Dorner, L.F. / Perona, J.J.
Citation
Journal: Biochemistry / Year: 2004
Title: Ca2+ binding in the active site of HincII: implications for the catalytic mechanism
Authors: Etzkorn, C. / Horton, N.C.
#1: Journal: Nat.Struct.Biol. / Year: 2002
Title: Sequence Selectivity and Degeneracy of a Restriction Endonuclease Mediated by DNA Intercalation
Authors: Horton, N.C. / Dorner, L.F. / Perona, J.J.
History
DepositionJul 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_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*CP*GP*AP*CP*CP*GP*G)-3'
F: 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
G: 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
H: 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
A: Type II restriction enzyme HindII
B: Type II restriction enzyme HindII
C: Type II restriction enzyme HindII
D: Type II restriction enzyme HindII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,34712
Polymers135,2558
Non-polymers924
Water13,926773
1
E: 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
F: 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
G: 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
A: Type II restriction enzyme HindII
B: Type II restriction enzyme HindII
C: Type II restriction enzyme HindII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5109
Polymers101,4416
Non-polymers693
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
G: 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
H: 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'
C: Type II restriction enzyme HindII
D: Type II restriction enzyme HindII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6677
Polymers71,6215
Non-polymers462
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.120, 177.670, 256.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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


Mass: 3993.586 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
Type II restriction enzyme HindII / Endonuclease HindII / R.HindII


Mass: 29820.066 Da / Num. of mol.: 4
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
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.78 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, citrate, sodium chloride, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2citrateCitric acid11
3sodium chloride11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 45516 / % possible obs: 86.6 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 16.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2291 5 %RANDOM
Rwork0.204 ---
obs-45516 86.6 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8067 1060 4 773 9904
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.13
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.245
X-RAY DIFFRACTIONc_mcangle_it2.104
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.747
LS refinement shellResolution: 2.5→2.52 Å / Total num. of bins used: 45
RfactorNum. reflection% reflection
Rfree0.374 40 4.9 %
Rwork0.3176 782 -
obs--75.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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