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- PDB-1na6: Crystal structure of restriction endonuclease EcoRII mutant R88A -

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Basic information

Entry
Database: PDB / ID: 1na6
TitleCrystal structure of restriction endonuclease EcoRII mutant R88A
ComponentsRestriction endonuclease EcoRII
KeywordsHYDROLASE / site-specific restriction / mutation / REPLICATION
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding
Similarity search - Function
Restriction endonuclease, type II, EcoRII, N-terminal / Restriction endonuclease EcoRII, N-terminal / Restriction Endonuclease - #80 / Restriction endonuclease, type II, EcoRII, C-terminal / EcoRII, C-terminal domain superfamily / EcoRII C terminal / DNA-binding pseudobarrel domain / At1g16640 B3 domain / DNA-binding pseudobarrel domain superfamily / Restriction Endonuclease ...Restriction endonuclease, type II, EcoRII, N-terminal / Restriction endonuclease EcoRII, N-terminal / Restriction Endonuclease - #80 / Restriction endonuclease, type II, EcoRII, C-terminal / EcoRII, C-terminal domain superfamily / EcoRII C terminal / DNA-binding pseudobarrel domain / At1g16640 B3 domain / DNA-binding pseudobarrel domain superfamily / Restriction Endonuclease / Restriction endonuclease type II-like / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Type II restriction enzyme EcoRII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
AuthorsZhou, X.E. / Wang, Y. / Reuter, M. / Mucke, M. / Kruger, D.H. / Meehan, E.J. / Chen, L.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold.
Authors: Zhou, X.E. / Wang, Y. / Reuter, M. / Mucke, M. / Kruger, D.H. / Meehan, E.J. / Chen, L.
History
DepositionNov 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Feb 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
A: Restriction endonuclease EcoRII
B: Restriction endonuclease EcoRII


Theoretical massNumber of molelcules
Total (without water)90,9152
Polymers90,9152
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-27 kcal/mol
Surface area34010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.746, 92.360, 88.308
Angle α, β, γ (deg.)90.00, 108.08, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein Restriction endonuclease EcoRII / E.C.3.1.21.4 / EcoRII / Type II restriction enzyme EcoRII / Endonuclease EcoRII / R.EcoRII


Mass: 45457.488 Da / Num. of mol.: 2 / Mutation: R88A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EcoRII / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: GenBank: 2961291, UniProt: P14633*PLUS, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 6.5 / PH range high: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMcacodylate1reservoirpH6.3-6.5
23.5-4 %(v/v)methanol1reservoir
335-40 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0088 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0088 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 50590 / Num. obs: 50590 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5178 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 52027 / % possible obs: 99.6 % / Num. measured all: 259113
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
ISIRASmodel building
CNS1refinement
HKL-2000data reduction
ISIRASphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 540623 / Data cutoff high rms absF: 540623 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2346 5 %Random
Rwork0.23 ---
all0.246 50590 --
obs0.236 46788 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.6908 Å2 / ksol: 0.361335 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å21.5 Å2
2---1.23 Å20 Å2
3----0.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6029 0 0 252 6281
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 342 5.5 %
Rwork0.24 5907 -
obs-5907 72.3 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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