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- PDB-1ev7: CRYSTAL STRUCTURE OF DNA RESTRICTION ENDONUCLEASE NAEI -

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Basic information

Entry
Database: PDB / ID: 1ev7
TitleCRYSTAL STRUCTURE OF DNA RESTRICTION ENDONUCLEASE NAEI
ComponentsTYPE IIE RESTRICTION ENDONUCLEASE NAEI
KeywordsHYDROLASE / apo-NaeI / restriction endonuclease / topoisomerase / helix-turn-helix / CAP
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
Type II restriction enzyme NaeI / Restriction endonuclease NaeI / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle ...Type II restriction enzyme NaeI / Restriction endonuclease NaeI / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Type II restriction enzyme NaeI
Similarity search - Component
Biological speciesLechevalieria aerocolonigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.38 Å
AuthorsHuai, Q. / Colandene, J.D. / Chen, Y. / Luo, F. / Zhao, Y.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase.
Authors: Huai, Q. / Colandene, J.D. / Chen, Y. / Luo, F. / Zhao, Y. / Topal, M.D. / Ke, H.
History
DepositionApr 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYPE IIE RESTRICTION ENDONUCLEASE NAEI
B: TYPE IIE RESTRICTION ENDONUCLEASE NAEI


Theoretical massNumber of molelcules
Total (without water)70,7682
Polymers70,7682
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-5 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.780, 56.160, 59.050
Angle α, β, γ (deg.)90.00, 95.92, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe deposited coordinates contain a biologically active dimer of NaeI

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Components

#1: Protein TYPE IIE RESTRICTION ENDONUCLEASE NAEI


Mass: 35384.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lechevalieria aerocolonigenes (bacteria)
Plasmid: PMALC2 / Production host: Escherichia coli (E. coli)
References: UniProt: P50187, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 6.1
Details: 20 mM malaic acid, 20 mM NaCl, 5 mM CaCl2, 1 mM 2-mercaptoethanol, 2% PEG3350, 1.5% ethanol, pH 6.1, MICRODIALYSIS, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMmalaic acid11
220 mM11NaCl
35 mM11CaCl2
41 mMbeta-mercaptoethanol11
52 %PEG335011
61.5 %ethanol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.978
DetectorType: BRANDEIS - B1 / Detector: CCD / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. all: 68874 / Num. obs: 25755 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.3
Reflection shellResolution: 2.38→2.48 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.185 / Num. unique all: 2118 / % possible all: 73.7
Reflection
*PLUS
Num. measured all: 68874
Reflection shell
*PLUS
% possible obs: 73.7 %

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.38→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: molecular dynamic refinement as implemented in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2868 2544 -Reflections were automatically selected by CNS
Rwork0.2375 ---
all-23128 --
obs-25672 79.2 %-
Refinement stepCycle: LAST / Resolution: 2.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 0 91 4711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3

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