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- PDB-6ukf: HhaI endonuclease in Complex with DNA at 1 Angstrom Resolution -

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Basic information

Entry
Database: PDB / ID: 6ukf
TitleHhaI endonuclease in Complex with DNA at 1 Angstrom Resolution
Components
  • DNA (5'-D(*CP*GP*(5IT)P*TP*GP*CP*GP*CP*TP*(5IT)P*GP*GP*A)-3')
  • DNA (5'-D(*TP*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*G)-3')
  • HhaI Restriction Endonuclease
KeywordsHYDROLASE/DNA / restriction / modification / protein-DNA complex / iodine phasing / HYDROLASE-DNA complex
Function / homologyACETATE ION / PHOSPHATE ION / DNA / DNA (> 10) / Uncharacterized protein
Function and homology information
Biological speciesHaemophilus parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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 ...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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_conn_type.id

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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(*TP*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*(5IT)P*TP*GP*CP*GP*CP*TP*(5IT)P*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,33222
Polymers38,1453
Non-polymers1,18719
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint14 kcal/mol
Surface area14520 Å2
Unit cell
Length a, b, c (Å)61.018, 37.317, 69.027
Angle α, β, γ (deg.)90.000, 109.768, 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(*TP*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*G)-3')


Mass: 3945.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus parahaemolyticus (bacteria)
#3: DNA chain DNA (5'-D(*CP*GP*(5IT)P*TP*GP*CP*GP*CP*TP*(5IT)P*GP*GP*A)-3')


Mass: 4222.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus parahaemolyticus (bacteria)

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Non-polymers , 5 types, 277 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 35% v/v 2-propanol, 0.1 M sodium phosphate dibasic / citric acid, pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1→26.4 Å / Num. obs: 148223 / % possible obs: 93.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.033 / Net I/σ(I): 16.3
Reflection shellResolution: 1→1.01 Å / Rmerge(I) obs: 1.069 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5385 / CC1/2: 0.378 / Rpim(I) all: 0.588

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Processing

Software
NameVersionClassification
SERGUIdata 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→26.39 Å / SU ML: 0.1108 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.6225
RfactorNum. reflection% reflection
Rfree0.1662 1997 1.35 %
Rwork0.1547 --
obs0.1549 148028 93.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.14 Å2
Refinement stepCycle: LAST / Resolution: 1→26.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 527 74 258 2936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00432850
X-RAY DIFFRACTIONf_angle_d0.82543939
X-RAY DIFFRACTIONf_chiral_restr0.0592418
X-RAY DIFFRACTIONf_plane_restr0.0041426
X-RAY DIFFRACTIONf_dihedral_angle_d21.99971085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.020.4293900.33566691X-RAY DIFFRACTION60.05
1.02-1.050.29311280.28239310X-RAY DIFFRACTION83.76
1.05-1.080.23521380.237910064X-RAY DIFFRACTION90.27
1.08-1.120.24021430.207910451X-RAY DIFFRACTION93.74
1.12-1.160.20171450.175410602X-RAY DIFFRACTION94.92
1.16-1.20.18141450.156210576X-RAY DIFFRACTION94.62
1.2-1.260.17091480.144310797X-RAY DIFFRACTION96.8
1.26-1.320.17291490.138810892X-RAY DIFFRACTION97.32
1.32-1.410.16261480.136410919X-RAY DIFFRACTION97.67
1.41-1.510.14261510.132410982X-RAY DIFFRACTION98.09
1.51-1.670.13721500.130310973X-RAY DIFFRACTION97.57
1.67-1.910.14541520.133611109X-RAY DIFFRACTION98.82
1.91-2.40.16791540.146111225X-RAY DIFFRACTION99.37
2.4-26.390.15611560.160511440X-RAY DIFFRACTION99.26

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