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Basic information

Entry
Database: PDB / ID: 2fkc
TitleCrystal Form I of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ion
Components
  • 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'
  • R.HinP1I restriction endonuclease
KeywordsHYDROLASE/DNA / RESTRICTION ENDONUCLEASE / PROTEIN DIMERIZATON / DNA SUPERHELIX / PROTEIN-DNA-METAL ION COMPLEX / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


endonuclease activity / metal ion binding
Similarity search - Function
Trna Endonuclease; Chain: A, domain 1 - #40 / Restriction endonuclease, type II, HinP1I / R.HinP1I restriction endonuclease / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / R.HinP1I restriction endonuclease
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsHorton, J.R.
Citation
Journal: Nucleic Acids Res. / Year: 2006
Title: DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.
Authors: Horton, J.R. / Zhang, X. / Maunus, R. / Yang, Z. / Wilson, G.G. / Roberts, R.J. / Cheng, X.
#1: Journal: Nucleic Acids Res. / Year: 2005
Title: Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI
Authors: Yang, Z. / Horton, J.R. / Maunus, R. / Wilson, G.G. / Roberts, R.J. / Cheng, X.
History
DepositionJan 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 30, 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_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.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.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_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

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'
D: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'
E: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'
F: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'
A: R.HinP1I restriction endonuclease
B: R.HinP1I restriction endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8889
Polymers69,7676
Non-polymers1203
Water79344
1
C: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'
D: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'
A: R.HinP1I restriction endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9645
Polymers34,8843
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'
F: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'
B: R.HinP1I restriction endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9244
Polymers34,8843
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.104, 105.104, 130.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 3045.992 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthesized Self-Annealing Oligonucleotide
#2: Protein R.HinP1I restriction endonuclease


Mass: 28791.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hinP1IR / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): PR1
References: GenBank: 57116674, UniProt: Q5I6E6*PLUS, type II site-specific deoxyribonuclease
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 7.5%(v/v) ethanol, 1.5M NaCl, 100mM Bis-Tris propane pH 7.8, and 20mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1ethanol11
2NaCl11
3Bis-Tris propane11
4CaCl211
5H2O11
6NaCl12
7CaCl212
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97179 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2005
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97179 Å / Relative weight: 1
ReflectionResolution: 2.39→19.89 Å / Num. all: 31659 / Num. obs: 31659 / % possible obs: 94.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 19
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.368 / Num. unique all: 3183 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
GLRFphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YNM

1ynm


Resolution: 2.39→19.89 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3124 -RANDOM
Rwork0.222 ---
all0.227 31659 --
obs0.226 31145 93.2 %-
Displacement parametersBiso mean: 59 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å2-0.63 Å20 Å2
2--1.41 Å20 Å2
3----3.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-19.89 Å
Luzzati sigma a0.39 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.39→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3981 808 3 44 4836
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d2.9

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