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- PDB-3mx1: The structure of GIY-YIG endonuclease R.Eco29kI -

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Basic information

Entry
Database: PDB / ID: 3mx1
TitleThe structure of GIY-YIG endonuclease R.Eco29kI
ComponentsEco29kIR
KeywordsHYDROLASE / type II restriction endonuclease / GIY-YIG endonuclease
Function / homologyRestriction endonuclease, type II, Eco29kI / Eco29kI restriction endonuclease / identical protein binding / Eco29kIR
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsMak, A.N.S. / Lambert, A.R. / Stoddard, B.L.
Citation
Journal: Structure / Year: 2010
Title: Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI.
Authors: Mak, A.N. / Lambert, A.R. / Stoddard, B.L.
#1: Journal: Nucleic Acids Res. / Year: 1992
Title: Eco29kI, a novel plasmid encoded restriction endonuclease from Escherichia coli.
Authors: Pertzev, A.V. / Ruban, N.M. / Zakharova, M.V. / Beletzkaja, I.V. / Petrov, S.I. / Kravetz, A.N. / Solonin, A.S.
History
DepositionMay 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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
Revision 1.3Apr 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
A: Eco29kIR


Theoretical massNumber of molelcules
Total (without water)26,7931
Polymers26,7931
Non-polymers00
Water3,063170
1
A: Eco29kIR

A: Eco29kIR


Theoretical massNumber of molelcules
Total (without water)53,5862
Polymers53,5862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3410 Å2
ΔGint-22 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.906, 90.074, 88.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Eco29kIR / Restriction endonuclease


Mass: 26792.988 Da / Num. of mol.: 1 / Mutation: E142Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eco29kIR / Plasmid: pET-15HE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS
References: UniProt: Q46944, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris HCl, 1.5M NaCl, 10% ethanol v/v, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.111
SYNCHROTRONALS 5.0.220.9801, 0.9802, 0.975
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 29, 2009
ADSC QUANTUM 3152CCDOct 28, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystalSINGLE WAVELENGTHMx-ray1
2single crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.98011
30.98021
40.9751
ReflectionResolution: 2.3→62.91 Å / Num. all: 15893 / Num. obs: 15078 / % possible obs: 98.82 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 18.35
Reflection shellResolution: 2.3→2.358 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 4.2 / % possible all: 94.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD
Starting model: Phase information by PHENIX

Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.695 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22781 791 5 %RANDOM
Rwork0.18285 ---
obs0.18507 15078 98.82 %-
all-15893 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--1.97 Å20 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 0 170 1810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0211689
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9282285
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6595207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55722.38184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52215256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8271514
X-RAY DIFFRACTIONr_chiral_restr0.1390.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211342
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2791.51023
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34621630
X-RAY DIFFRACTIONr_scbond_it3.383666
X-RAY DIFFRACTIONr_scangle_it5.2914.5655
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 50 -
Rwork0.196 1035 -
obs--92.42 %
Refinement TLS params.Method: refined / Origin x: -4.0849 Å / Origin y: -28.6984 Å / Origin z: -5.2304 Å
111213212223313233
T0.2605 Å20.0895 Å20.0245 Å2-0.1151 Å20.0065 Å2--0.1441 Å2
L0.9659 °2-0.0543 °20.3847 °2-0.6279 °20.4883 °2--4.0157 °2
S-0.0947 Å °-0.0395 Å °0.2065 Å °-0.0746 Å °0.103 Å °-0.0059 Å °-1.006 Å °-0.3126 Å °-0.0083 Å °

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