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- PDB-1yfi: Crystal Structure of restriction endonuclease MspI in complex wit... -

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Basic information

Entry
Database: PDB / ID: 1yfi
TitleCrystal Structure of restriction endonuclease MspI in complex with its cognate DNA in P212121 space group
Components
  • 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
  • Type II restriction enzyme MspI
KeywordsHydrolase/DNA / protein-DNA complex / Hydrolase-DNA COMPLEX
Function / homologyRestriction endonuclease, type II, MspI / Restriction endonuclease MspI / type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / Restriction endonuclease type II-like / DNA binding / DNA / Type II restriction enzyme MspI
Function and homology information
Biological speciesMoraxella sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsXu, Q.S. / Kucera, R.B. / Roberts, R.J. / Guo, H.-C.
CitationJournal: Protein Sci. / Year: 2005
Title: Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure.
Authors: Xu, Q.S. / Roberts, R.J. / Guo, H.-C.
History
DepositionJan 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
C: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
D: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
E: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
F: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
A: Type II restriction enzyme MspI
B: Type II restriction enzyme MspI


Theoretical massNumber of molelcules
Total (without water)71,9406
Polymers71,9406
Non-polymers00
Water95553
1
C: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
D: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
A: Type II restriction enzyme MspI


Theoretical massNumber of molelcules
Total (without water)35,9703
Polymers35,9703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
F: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
B: Type II restriction enzyme MspI


Theoretical massNumber of molelcules
Total (without water)35,9703
Polymers35,9703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.295, 111.266, 130.735
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
5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'


Mass: 3046.980 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein Type II restriction enzyme MspI / Endonuclease MspI / R.MspI


Mass: 29876.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella sp. (bacteria) / Gene: mspIR / Plasmid: PCAD39 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2502
References: UniProt: P11405, type II site-specific deoxyribonuclease
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.58 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, ammonium sulfate, calcium chloride, PEG 8000, glycerol , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2ammonium sulfate11
3PEG 800011
4glycerol11
5water11
6MES12
7ammonium sulfate12
8PEG 800012
9glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.904 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Apr 8, 2001
Details: DOUBLE-CRYSTAL MONOCHROMATOR SI(111), BEAM FOCUSED BY A TOROIDAL MIRROR
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR Si(111) MIRROR + NI FILTER
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.904 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. all: 21426 / Num. obs: 21426 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 28.7
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 7 / Num. unique all: 2100 / Rsym value: 0.282 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SA3

1sa3


Resolution: 2.7→46.94 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1435032.38 / Data cutoff high rms absF: 1435032.38 / 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
Rfree0.274 2088 10 %RANDOM
Rwork0.226 ---
all0.231 20877 --
obs0.226 20877 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.318155 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.08 Å20 Å20 Å2
2--1.47 Å20 Å2
3---1.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.7→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 767 0 53 5035
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.741.5
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scbond_it2.842
X-RAY DIFFRACTIONc_scangle_it4.112.5
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.37 182 8.7 %
Rwork0.314 1904 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3DNA-RNA_REP.PARAMWATER.TOP

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