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- PDB-1yf2: Three-dimensional structure of DNA sequence specificity (S) subun... -

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Basic information

Entry
Database: PDB / ID: 1yf2
TitleThree-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications
ComponentsType I restriction-modification enzyme, S subunit
KeywordsHYDROLASE REGULATOR / Type I restriction modification enzyme / S-subunit / Structural genomics / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homologyRestriction endonuclease, type I, HsdS / Type I restriction modification DNA specificity domain / DNA restriction-modification system / DNA binding / Type-1 restriction enzyme MjaXIP specificity protein
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKim, J.S. / Degiovanni, A. / Jancarik, J. / Adams, P.D. / Yokota, H.A. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications.
Authors: Kim, J.S. / Degiovanni, A. / Jancarik, J. / Adams, P.D. / Yokota, H. / Kim, R. / Kim, S.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 30, 2004 / Release: Feb 15, 2005
RevisionDateData content typeGroupProviderType
1.0Feb 15, 2005Structure modelrepositoryInitial release
1.1Apr 30, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelSource and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type I restriction-modification enzyme, S subunit
B: Type I restriction-modification enzyme, S subunit


Theoretical massNumber of molelcules
Total (without water)97,2792
Polymers97,2792
Non-polymers00
Water5,927329
1
A: Type I restriction-modification enzyme, S subunit


Theoretical massNumber of molelcules
Total (without water)48,6401
Polymers48,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type I restriction-modification enzyme, S subunit


Theoretical massNumber of molelcules
Total (without water)48,6401
Polymers48,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)71.972, 94.222, 103.520
Angle α, β, γ (deg.)90.00, 95.01, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer

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Components

#1: Protein/peptide Type I restriction-modification enzyme, S subunit


Mass: 48639.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Plasmid details: pET23a derivatized expression vector / Plasmid: pB3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57594
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 3.74 Å3/Da / Density % sol: 66.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 3000, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2004 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. all: 69051 / Num. obs: 59867 / Observed criterion σ(F): 1.2 / Observed criterion σ(I): 1.2 / Biso Wilson estimate: 49.2 Å2
Reflection shellResolution: 2.21→2.29 Å / % possible all: 26.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→48.52 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 361731.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 5128 10.1 %RANDOM
Rwork0.236 ---
Obs0.236 50597 93.7 %-
All-53699 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.6471 Å2 / ksol: 0.311875 e/Å3
Displacement parametersBiso mean: 74.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.8 Å20 Å20.53 Å2
2--0.34 Å20 Å2
3---5.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6828 0 0 329 7157
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
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
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.413 765 10.3 %
Rwork0.365 6650 -
Obs--83.2 %
Xplor file

Refinement-ID: X-RAY DIFFRACTION

Serial noParam fileTopol file
1PROTEIN_REP.PARAMPROTEIN.TOP
2WATER_REP.PARAMWATER.TOP

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