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- PDB-1stx: Structure of the K38A mutant of EcoRV bound to cognate DNA and Mn2+ -

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Basic information

Entry
Database: PDB / ID: 1stx
TitleStructure of the K38A mutant of EcoRV bound to cognate DNA and Mn2+
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 / restriction enzyme / EcoRV / DNA / X-ray crystallography / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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)63,95412
Polymers63,6256
Non-polymers3306
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.710, 58.690, 82.100
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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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 / E.C.3.1.21.4 / Endonuclease EcoRV / R.EcoRV / type II site-specific deoxyribonuclease EcoRV


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


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: 17% PEG 4000, 0.1M HEPES pH 7.5, 0.15M NaCl 50mM MnCl2, Vapor diffusion, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2HEPES11
3NaClSodium chloride11
4MnCl211
5PEG 400012
6HEPES12
7NaClSodium chloride12
8MnCl212

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 33633 / Num. obs: 32988

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Processing

Software
NameClassification
CNSrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 683 5 %random
Rwork0.201 ---
obs0.2012 32988 99.2 %-
all-33633 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.832 Å20 Å2-5.629 Å2
2---0.141 Å20 Å2
3----8.691 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3969 448 6 383 4806
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg2.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_scbond_it1.9672
X-RAY DIFFRACTIONc_mcangle_it2.2252
X-RAY DIFFRACTIONc_scangle_it2.8722.5

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