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- PDB-1iaw: CRYSTAL STRUCTURE OF NAEI COMPLEXED WITH 17MER DNA -

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Basic information

Entry
Database: PDB / ID: 1iaw
TitleCRYSTAL STRUCTURE OF NAEI COMPLEXED WITH 17MER DNA
Components
  • 5'-D(*TP*GP*CP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*GP*GP*C)-3'
  • TYPE II RESTRICTION ENZYME NAEI
KeywordsHYDROLASE/DNA / 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
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
DNA / DNA (> 10) / Type II restriction enzyme NaeI
Similarity search - Component
Biological speciesLechevalieria aerocolonigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHuai, Q. / Colandene, J.D. / Topal, M.D. / Ke, H.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement.
Authors: Huai, Q. / Colandene, J.D. / Topal, M.D. / Ke, H.
History
DepositionMar 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Other
Revision 1.4Feb 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-D(*TP*GP*CP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*GP*GP*C)-3'
D: 5'-D(*TP*GP*CP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*GP*GP*C)-3'
E: 5'-D(*TP*GP*CP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*GP*GP*C)-3'
F: 5'-D(*TP*GP*CP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*GP*GP*C)-3'
A: TYPE II RESTRICTION ENZYME NAEI
B: TYPE II RESTRICTION ENZYME NAEI


Theoretical massNumber of molelcules
Total (without water)91,5896
Polymers91,5896
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.6, 65.0, 258.5
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain
5'-D(*TP*GP*CP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*GP*GP*C)-3'


Mass: 5205.349 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein TYPE II RESTRICTION ENZYME NAEI


Mass: 35384.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lechevalieria aerocolonigenes (bacteria)
Gene: NAE I / Plasmid: PMALE2 / Production host: Escherichia coli (E. coli) / Strain (production host): CAA1
References: UniProt: P50187, type II site-specific deoxyribonuclease
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 296 K / Method: evaporation / pH: 5.6
Details: 20% PEG3350, 0.1 M Na citrate, 0.2 M ammonium chloride, 10% MPD, pH 5.6, EVAPORATION, temperature 296K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG335011
2sodium citrate11
3ammonium chloride11
4MPD11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorDetector: CCD / Date: Aug 3, 2000
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→99 Å / Num. all: 32365 / Num. obs: 120725 / % possible obs: 80.4 % / Observed criterion σ(F): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.2
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.8 / % possible all: 36.1

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unligated NaeI

Resolution: 2.4→99 Å / Isotropic thermal model: iostropic / σ(F): 0 / Stereochemistry target values: defined by program CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.293 3060 -selected by program CNS
Rwork0.243 ---
all0.243 40302 --
obs-30706 76.2 %-
Displacement parametersBiso mean: 37.2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 1375 0 44 6195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.35
X-RAY DIFFRACTIONx_bond_d0.0065

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