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- PDB-5hlk: Crystal structure of the ternary EcoRV-DNA-Lu complex with cleave... -

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Basic information

Entry
Database: PDB / ID: 5hlk
TitleCrystal structure of the ternary EcoRV-DNA-Lu complex with cleaved DNA substrate.
Components
  • DNA (5'-D(*AP*AP*AP*GP*AP*TP)-3')
  • DNA (5'-D(*AP*TP*CP*TP*TP*TP)-3')
  • Type-2 restriction enzyme EcoRV
KeywordsHYDROLASE/DNA / Hydrolase / Protein-DNA complex / Lutetium / 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 / metal ion binding
Similarity search - Function
Restriction endonuclease, type II, EcoRV / Restriction endonuclease, type II, EcoRV, Proteobacteria / Restriction endonuclease EcoRV / 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 EcoRV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSangani, S.S. / Kehr, A.D. / Sinha, K. / Rule, G.S. / Jen-Jacobson, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM029207 United States
CitationJournal: Biochemistry / Year: 2016
Title: Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex.
Authors: Sinha, K. / Sangani, S.S. / Kehr, A.D. / Rule, G.S. / Jen-Jacobson, L.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionNov 9, 2016ID: 4ORJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type-2 restriction enzyme EcoRV
B: Type-2 restriction enzyme EcoRV
C: DNA (5'-D(*AP*AP*AP*GP*AP*TP)-3')
D: DNA (5'-D(*AP*AP*AP*GP*AP*TP)-3')
E: DNA (5'-D(*AP*TP*CP*TP*TP*TP)-3')
F: DNA (5'-D(*AP*TP*CP*TP*TP*TP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,57621
Polymers64,3496
Non-polymers1,22615
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-49 kcal/mol
Surface area22230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.621, 48.327, 63.531
Angle α, β, γ (deg.)96.94, 108.78, 106.70
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Type-2 restriction enzyme EcoRV / R.EcoRV / Endonuclease EcoRV / Type II restriction enzyme EcoRV


Mass: 28559.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ecoRVR / Production host: Escherichia coli (E. coli)
References: UniProt: P04390, type II site-specific deoxyribonuclease

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DNA chain , 2 types, 4 molecules CDEF

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


Mass: 1841.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*TP*CP*TP*TP*TP)-3')


Mass: 1774.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 252 molecules

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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#6: Chemical
ChemComp-LU / LUTETIUM (III) ION / LU


Mass: 174.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Lu
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 9.4 mg/mL, 3:3 Enzyme:Well, 100 mM HEPES pH 7.5, 8% Ethylene glycol, 7% Polyethylene glycol 8000, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→58.46 Å / Num. obs: 28737 / % possible obs: 78.9 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.051 / Rsym value: 0.057 / Net I/σ(I): 20.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 2.7 / % possible all: 12

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLM7.2.1data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B94

1b94


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.624 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.22832 1365 4.9 %RANDOM
Rwork0.16553 ---
obs0.16858 26617 82.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.437 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-1.03 Å2-0.79 Å2
2--2.48 Å2-0.25 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 468 36 237 4787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194708
X-RAY DIFFRACTIONr_bond_other_d0.0020.024200
X-RAY DIFFRACTIONr_angle_refined_deg1.781.8526452
X-RAY DIFFRACTIONr_angle_other_deg1.14639695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.955492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57624.299214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10715738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9971522
X-RAY DIFFRACTIONr_chiral_restr0.1160.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024979
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021111
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9441.9691956
X-RAY DIFFRACTIONr_mcbond_other1.9441.9691955
X-RAY DIFFRACTIONr_mcangle_it3.1722.9452443
X-RAY DIFFRACTIONr_mcangle_other3.1712.9462444
X-RAY DIFFRACTIONr_scbond_it2.4632.4412752
X-RAY DIFFRACTIONr_scbond_other2.462.4382751
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0023.5924007
X-RAY DIFFRACTIONr_long_range_B_refined6.61617.9775798
X-RAY DIFFRACTIONr_long_range_B_other6.61417.965797
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 36 -
Rwork0.2 507 -
obs--21.79 %

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