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- PDB-6ukg: HhaI endonuclease in Complex With DNA in space group P21 (pH 4.2) -

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Basic information

Entry
Database: PDB / ID: 6ukg
TitleHhaI endonuclease in Complex With DNA in space group P21 (pH 4.2)
Components
  • DNA (5'-D(*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*AP*G)-3')
  • DNA (5'-D(*CP*TP*GP*TP*TP*GP*CP*GP*CP*TP*TP*GP*GP*A)-3')
  • HhaI Restriction Endonuclease
KeywordsHYDROLASE/DNA / restriction / modification / protein-DNA complex / iodine phasing / HYDROLASE-DNA complex
Function / homologyPHOSPHATE ION / DNA / DNA (> 10) / Uncharacterized protein
Function and homology information
Biological speciesHaemophilus parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsHorton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 angstrom.
Authors: Horton, J.R. / Yang, J. / Zhang, X. / Petronzio, T. / Fomenkov, A. / Wilson, G.G. / Roberts, R.J. / Cheng, X.
History
DepositionOct 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: HhaI Restriction Endonuclease
A: DNA (5'-D(*CP*TP*GP*TP*TP*GP*CP*GP*CP*TP*TP*GP*GP*A)-3')
B: DNA (5'-D(*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0129
Polymers38,5393
Non-polymers4736
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-33 kcal/mol
Surface area15280 Å2
Unit cell
Length a, b, c (Å)61.849, 37.545, 69.923
Angle α, β, γ (deg.)90.000, 110.256, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules X

#1: Protein HhaI Restriction Endonuclease


Mass: 29977.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus parahaemolyticus (bacteria)
Gene: HMPREF1050_0931 / Production host: Escherichia coli (E. coli) / References: UniProt: I3DBY6, Hydrolases

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DNA chain , 2 types, 2 molecules AB

#2: DNA chain DNA (5'-D(*CP*TP*GP*TP*TP*GP*CP*GP*CP*TP*TP*GP*GP*A)-3')


Mass: 4302.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus parahaemolyticus (bacteria)
#3: DNA chain DNA (5'-D(*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*AP*G)-3')


Mass: 4258.796 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus parahaemolyticus (bacteria)

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Non-polymers , 4 types, 276 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 10% v/v 2-propanol, sodium phosphate / citric acid, pH 4.2, 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→31.52 Å / Num. obs: 192216 / % possible obs: 88.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Net I/σ(I): 14.5
Reflection shellResolution: 1.16→1.21 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 12298 / CC1/2: 0.863 / Rpim(I) all: 0.217 / % possible all: 66.5

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Processing

Software
NameVersionClassification
SERGUI1.15.2_3472data collection
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6UKE

6uke


Resolution: 1.16→31.52 Å / SU ML: 0.0732 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 13.6081
RfactorNum. reflection% reflection
Rfree0.1572 3656 2.01 %
Rwork0.1409 --
obs0.1412 181702 88.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.21 Å2
Refinement stepCycle: LAST / Resolution: 1.16→31.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 894 27 270 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733224
X-RAY DIFFRACTIONf_angle_d0.99564552
X-RAY DIFFRACTIONf_chiral_restr0.0703490
X-RAY DIFFRACTIONf_plane_restr0.0075439
X-RAY DIFFRACTIONf_dihedral_angle_d22.81421263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.180.2544730.2473720X-RAY DIFFRACTION48.02
1.18-1.190.21471000.22694680X-RAY DIFFRACTION60.68
1.19-1.210.19441110.20025448X-RAY DIFFRACTION70.55
1.21-1.230.1851260.19326304X-RAY DIFFRACTION81.85
1.23-1.250.20381450.16737289X-RAY DIFFRACTION94.45
1.25-1.270.1921590.15587583X-RAY DIFFRACTION98.85
1.27-1.290.14971550.15267633X-RAY DIFFRACTION98.95
1.29-1.310.1411550.14917548X-RAY DIFFRACTION98.77
1.31-1.340.18271550.14417645X-RAY DIFFRACTION98.7
1.34-1.360.15811580.13597597X-RAY DIFFRACTION98.9
1.36-1.390.17641600.12937686X-RAY DIFFRACTION98.78
1.39-1.430.12791530.12257567X-RAY DIFFRACTION98.7
1.43-1.460.15671530.12257522X-RAY DIFFRACTION97.95
1.46-1.50.14481580.11667604X-RAY DIFFRACTION98.6
1.5-1.550.1341570.11177661X-RAY DIFFRACTION99.21
1.55-1.60.13881580.10627621X-RAY DIFFRACTION99.46
1.6-1.650.11991610.10727689X-RAY DIFFRACTION99.54
1.65-1.720.14431590.11277683X-RAY DIFFRACTION99.35
1.72-1.80.12521590.11317616X-RAY DIFFRACTION99.16
1.8-1.890.13911430.12347067X-RAY DIFFRACTION92.05
1.89-2.010.1491940.13034461X-RAY DIFFRACTION57.95
2.01-2.160.13341580.13427639X-RAY DIFFRACTION99.55
2.16-2.380.1628940.13754669X-RAY DIFFRACTION60.56
2.38-2.730.1621550.14957657X-RAY DIFFRACTION99.66
2.73-3.440.14791480.15477322X-RAY DIFFRACTION94.68
3.44-31.520.20091090.16525135X-RAY DIFFRACTION66.74

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