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- PDB-3c25: Crystal Structure of NotI Restriction Endonuclease Bound to Cogna... -

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Basic information

Entry
Database: PDB / ID: 3c25
TitleCrystal Structure of NotI Restriction Endonuclease Bound to Cognate DNA
Components
  • DNA (5'-D(*DCP*DGP*DGP*DAP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DGP*DCP*DCP*DG)-3')
  • DNA (5'-D(*DCP*DGP*DGP*DCP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DTP*DCP*DCP*DG)-3')
  • NotI restriction endonuclease
Keywordshydrolase/DNA / Protein-DNA complex / Restriction enzyme fold / PD-(D/E)-XK / Restriction endonuclease / rare-cutting / Fe-Cys4 motif / iron-sulfur protein / hydrolase-DNA COMPLEX
Function / homologyendonuclease activity / identical protein binding / metal ion binding / : / DNA / DNA (> 10) / NotI restriction endonuclease
Function and homology information
Biological speciesNocardia otitidiscaviarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLambert, A.R. / Sussman, D. / Shen, B. / Stoddard, B.L.
CitationJournal: Structure / Year: 2008
Title: Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding.
Authors: Lambert, A.R. / Sussman, D. / Shen, B. / Maunus, R. / Nix, J. / Samuelson, J. / Xu, S.Y. / Stoddard, B.L.
History
DepositionJan 24, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 12, 2008ID: 3BVR
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*DCP*DGP*DGP*DAP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DGP*DCP*DCP*DG)-3')
D: DNA (5'-D(*DCP*DGP*DGP*DCP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DTP*DCP*DCP*DG)-3')
A: NotI restriction endonuclease
B: NotI restriction endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,72910
Polymers98,4574
Non-polymers2726
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.890, 81.712, 73.583
Angle α, β, γ (deg.)90.000, 99.510, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 12 - 364 / Label seq-ID: 12 - 364

Dom-IDAuth asym-IDLabel asym-ID
1AC
2BD

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Components

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DNA chain , 2 types, 2 molecules CD

#1: DNA chain DNA (5'-D(*DCP*DGP*DGP*DAP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DGP*DCP*DCP*DG)-3')


Mass: 6781.330 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic DNA construct containing cognate recognition sequence of NotI
#2: DNA chain DNA (5'-D(*DCP*DGP*DGP*DCP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DTP*DCP*DCP*DG)-3')


Mass: 6732.292 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic DNA construct containing cognate recognition sequence of NotI

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Protein , 1 types, 2 molecules AB

#3: Protein NotI restriction endonuclease


Mass: 42471.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia otitidiscaviarum (bacteria) / Gene: notIR / Production host: Escherichia coli (E. coli) / References: UniProt: Q2I6W2

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Non-polymers , 3 types, 174 molecules

#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.23 Å3/Da / Density % sol: 44.72 %
Crystal growpH: 6.5
Details: 2.0 M Ammonium Sulfate, 100 mM MES, 20 mM NaCl, 10 mM CaCl2, pH 6.5
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Sulfate11
2MES11
3NaCl11
4CaCl211
5Ammonium Sulfate12
6MES12
7NaCl12
8CaCl212

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.5 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 29547 / % possible obs: 97.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.055 / Χ2: 0.932 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5950.27724570.668182.2
2.59-2.695.90.24628840.698195.5
2.69-2.826.90.1930110.726199.6
2.82-2.967.30.13630140.8341100
2.96-3.157.40.129920.9781100
3.15-3.397.40.07330101.0531100
3.39-3.737.30.06230221.0311100
3.73-4.277.20.04930161.0731100
4.27-5.387.20.03730500.9271100
5.38-507.30.04730911.126199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementResolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU B: 25.676 / SU ML: 0.292 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.071 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1483 5.1 %RANDOM
Rwork0.223 ---
obs0.226 29363 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.001 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å2-1.63 Å2
2--2.04 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5438 896 6 168 6508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226598
X-RAY DIFFRACTIONr_angle_refined_deg1.0942.1239164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.035705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11823.061245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41415830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0671540
X-RAY DIFFRACTIONr_chiral_restr0.0850.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024804
X-RAY DIFFRACTIONr_nbd_refined0.1720.22918
X-RAY DIFFRACTIONr_nbtor_refined0.2950.24368
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2305
X-RAY DIFFRACTIONr_metal_ion_refined0.0080.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0710.28
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0110.21
X-RAY DIFFRACTIONr_mcbond_it0.1481.53609
X-RAY DIFFRACTIONr_mcangle_it0.26125661
X-RAY DIFFRACTIONr_scbond_it0.35633755
X-RAY DIFFRACTIONr_scangle_it0.5824.53503
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2668 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.340.5
MEDIUM THERMAL0.122
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 86 -
Rwork0.303 1691 -
all-1777 -
obs--80.3 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.30480.25891.79024.0368-0.09093.7351-0.0592-0.0710.0533-0.4246-0.16620.7884-0.3914-0.92690.2254-0.31050.2084-0.0601-0.1483-0.1004-0.2494-31.48520.5284-20.2985
23.45270.62041.71163.84250.84754.3403-0.03460.5971-0.1147-0.15110.0404-1.4514-0.50270.9188-0.0058-0.3216-0.12660.0728-0.21870.07440.1386-0.32132.2965-16.1902
34.95270.1111.4755.82730.80646.01750.15370.2657-0.4749-0.2714-0.0092-0.32420.0547-0.0937-0.1444-0.47110.01680.0643-0.3687-0.0036-0.2835-15.5221-6.5224-18.0674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC12 - 36312 - 363
2X-RAY DIFFRACTION2BD12 - 36312 - 363
3X-RAY DIFFRACTION3CA1 - 221 - 22
4X-RAY DIFFRACTION3DB1 - 221 - 22

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