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- PDB-1sx5: K38A EcoRV bound to cleaved DNA and Mn2+: P1 crystal form -

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Basic information

Entry
Database: PDB / ID: 1sx5
TitleK38A EcoRV bound to cleaved DNA and Mn2+: P1 crystal form
Components
  • 5'-D(*AP*AP*AP*GP*AP*T)-3'
  • 5'-D(P*AP*TP*CP*TP*T)-3'
  • Type II restriction enzyme EcoRV
KeywordsHYDROLASE/DNA / endonuclease / protein-DNA complex / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHorton, N.C. / Perona, J.J.
CitationJournal: Biochemistry / Year: 2004
Title: DNA cleavage by EcoRV endonuclease: Two metal ions in three metal ion binding sites
Authors: Horton, N.C. / Perona, J.J.
History
DepositionMar 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 28, 2021Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine ...pdbx_struct_conn_angle / refine / reflns / reflns_shell / struct_conn / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._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 / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _reflns.percent_possible_obs / _reflns_shell.percent_possible_all / _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
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-D(*AP*AP*AP*GP*AP*T)-3'
D: 5'-D(P*AP*TP*CP*TP*T)-3'
E: 5'-D(*AP*AP*AP*GP*AP*T)-3'
F: 5'-D(P*AP*TP*CP*TP*T)-3'
A: Type II restriction enzyme EcoRV
B: Type II restriction enzyme EcoRV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,11915
Polymers63,6256
Non-polymers4949
Water6,702372
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.708, 48.627, 63.544
Angle α, β, γ (deg.)96.68, 108.94, 107.33
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain 5'-D(*AP*AP*AP*GP*AP*T)-3'


Mass: 1841.268 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*AP*TP*CP*TP*T)-3'


Mass: 1470.010 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein Type II restriction enzyme EcoRV / Endonuclease EcoRV / R.EcoRV


Mass: 28501.053 Da / Num. of mol.: 2 / Mutation: K38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECORVR / Plasmid: pBSRV / Production host: Escherichia coli (E. coli) / Strain (production host): MM294 (endI-, pro-, thi-, rk-mk+)
References: UniProt: P04390, type II site-specific deoxyribonuclease
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 315 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, 0.1M HEPES, 0.15M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 315K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2HEPES12
3NaClSodium chloride13

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 80255 / Num. obs: 74930 / % possible obs: 93 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 9.5
Reflection shellResolution: 1.5→1.51 Å / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2 / Rsym value: 0.327 / % possible all: 92.3

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Processing

Software
NameClassification
MOSFLMdata reduction
X-PLORmodel building
CNSrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→20 Å / Cross valid method: FREE R-VALUE / σ(F): 3 / σ(I): 0 / Stereochemistry target values: cns
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3791 -random 5%
Rwork0.214 ---
all-80255 --
obs-74930 93 %-
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 448 9 372 4693
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_dev1.91

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