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- PDB-1d02: CRYSTAL STRUCTURE OF MUNI RESTRICTION ENDONUCLEASE IN COMPLEX WIT... -

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Basic information

Entry
Database: PDB / ID: 1d02
TitleCRYSTAL STRUCTURE OF MUNI RESTRICTION ENDONUCLEASE IN COMPLEX WITH COGNATE DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*AP*TP*TP*GP*GP*C)-3')
  • TYPE II RESTRICTION ENZYME MUNI
KeywordsHYDROLASE/DNA / ALPHA/BETA PROTEIN / PROTEIN-DNA COMPLEX / DISTORTED DOUBLE HELIX / 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 MunI / Type II restriction enzyme MunI / ECO RI Endonuclease; Chain A / Eco RI Endonuclease, subunit A / Restriction endonuclease, type II, EcoRI/MunI / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Type II restriction enzyme MunI
Similarity search - Component
Biological speciesMycoplasma (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsDeibert, M. / Grazulis, S. / Janulaitis, A. / Siksnys, V. / Huber, R.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution.
Authors: Deibert, M. / Grazulis, S. / Janulaitis, A. / Siksnys, V. / Huber, R.
History
DepositionSep 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,8434
Polymers52,8434
Non-polymers00
Water11,638646
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.400, 72.470, 121.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DECAMERIC OLIGONUCLEOTIDE 5'-DS(GPCPCPAPAPTPTPGPGPC) WAS SYNTHESIZED WITH STANDARD PROCEDURES
#2: Protein TYPE II RESTRICTION ENZYME MUNI / ENDONUCLEASE MUNI


Mass: 23376.451 Da / Num. of mol.: 2 / Mutation: D83A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma (bacteria) / Genus: Mycoplasma / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267
References: UniProt: P43642, type II site-specific deoxyribonuclease
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 8000, CALCIUM CHLORIDE, SODIUM CHLORIDE, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 mMprotein1drop
214 %PEG80001reservoir
3200 mM1reservoirNaCl
450 mM1reservoirCaCl2
50.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.006
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 1.7→8 Å / Num. all: 177834 / Num. obs: 56945 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.052
Reflection
*PLUS
Num. measured all: 177834
Reflection shell
*PLUS
% possible obs: 84 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.7→8 Å / σ(F): 2
Stereochemistry target values: ENGH & HUBER (PROTEIN), PARKINSON (DNA)
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2650 -RANDOM, 5%
Rwork0.18 ---
obs0.18 56945 92.4 %-
all-52617 --
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 404 0 646 4312
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.49
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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