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- PDB-3mis: I-MsoI re-designed for altered DNA cleavage specificity (-8G) -

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Basic information

Entry
Database: PDB / ID: 3mis
TitleI-MsoI re-designed for altered DNA cleavage specificity (-8G)
Components
  • DNA (5'-D(*CP*GP*GP*AP*GP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*CP*CP*TP*GP*C)-3')
  • DNA (5'-D(*GP*CP*AP*GP*GP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*CP*TP*CP*CP*G)-3')
  • Mso-8G
KeywordsDE NOVO PROTEIN/DNA / protein-DNA complex / homing nuclease / Rosetta design / DE NOVO PROTEIN-DNA complex
Function / homologyHoming endonucleases / Endonuclease I-creI / Roll / Alpha Beta / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTaylor, G.K. / Stoddard, B.L.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.
Authors: Ashworth, J. / Taylor, G.K. / Havranek, J.J. / Quadri, S.A. / Stoddard, B.L. / Baker, D.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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
A: Mso-8G
B: Mso-8G
C: DNA (5'-D(*GP*CP*AP*GP*GP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*CP*TP*CP*CP*G)-3')
D: DNA (5'-D(*CP*GP*GP*AP*GP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*CP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1257
Polymers52,0044
Non-polymers1203
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-91 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.589, 42.632, 71.577
Angle α, β, γ (deg.)72.86, 72.83, 71.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Mso-8G


Mass: 18630.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Strain: oke-1 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
#2: DNA chain DNA (5'-D(*GP*CP*AP*GP*GP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*CP*TP*CP*CP*G)-3')


Mass: 7420.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: top strand oligonucleotide target
#3: DNA chain DNA (5'-D(*CP*GP*GP*AP*GP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*CP*CP*TP*GP*C)-3')


Mass: 7322.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: bottom strand oligonucleotide target
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 24% PEG 4000, 100mM Tris, 20mM NaCl, 5mM CaCl2 , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 1, 2008 / Details: Confocal Varimax Optics Systems
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→23.25 Å / Num. all: 19727 / Num. obs: 18927 / % possible obs: 95.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.92 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.87 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1979 / % possible all: 90.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1m5x

1m5x


Resolution: 2.3→23.247 Å / SU ML: 0.42 / σ(F): 1.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3078 980 5.2 %random
Rwork0.2456 ---
obs0.2488 18859 --
all-19727 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.763 Å2 / ksol: 0.312 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→23.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2632 978 3 93 3706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073778
X-RAY DIFFRACTIONf_angle_d1.1385304
X-RAY DIFFRACTIONf_dihedral_angle_d21.6461500
X-RAY DIFFRACTIONf_chiral_restr0.061586
X-RAY DIFFRACTIONf_plane_restr0.004514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID
2.3-2.42120.33931500.30462412X-RAY DIFFRACTION
2.4212-2.57270.37531230.30542557X-RAY DIFFRACTION
2.5727-2.7710.35241430.29592535X-RAY DIFFRACTION
2.771-3.04940.37131350.29962583X-RAY DIFFRACTION
3.0494-3.48930.33241360.25842578X-RAY DIFFRACTION
3.4893-4.39130.2971350.22172608X-RAY DIFFRACTION
4.3913-23.24820.24311580.17582606X-RAY DIFFRACTION
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined2.6711-3.78390.67523.5639-4.02618.25810.1581-0.12010.4156-0.2392-0.2425-0.55960.93531.08040.150.21230.0434-0.10570.2254-0.07920.4344.7797-12.9073-8.0029
25.2910.8738-0.71651.3154-1.26791.83021.4380.57350.44570.10260.74190.1049-0.4673-1.111-0.99851.26820.12550.25920.82860.16510.7998
30.9276-0.554-1.32173.2019-1.3248.8640.48490.00650.1298-0.0215-0.1681-0.4906-0.3181.5694-0.34540.2003-0.1989-0.05180.4407-0.12520.3514
49.58140.3012-1.44735.20852.41965.9123-0.12461.9457-0.7707-1.91750.3974-0.15181.2297-1.7808-0.64180.8593-0.1537-0.31410.4618-0.11460.3042
53.21380.0891-0.81113.07710.16656.52130.6991.40260.4803-0.8307-0.2280.1030.1412-2.9314-0.15550.31380.2448-0.10491.27630.10240.3248
62.924-4.4722-4.96497.93936.74988.0285-0.7504-0.3123-0.75111.04070.56820.57261.88970.73740.12610.4180.0693-0.09790.2335-0.0310.4938
72.21390.2168-1.70733.0708-0.63762.2432-0.39880.46091.140.91391.12030.16910.4280.6545-0.311.37290.47590.49590.93550.15440.8725
81.9578-0.1328-2.59613.7982-2.05678.4285-0.36020.1749-0.05460.17750.75810.32521.1067-1.1494-0.44390.1948-0.2163-0.13780.36160.04330.3421
97.99392.3569-1.60927.7555-5.51893.4910.9338-1.117-1.05541.2861-0.1451-0.3389-0.5321.5687-0.35450.3423-0.0421-0.24120.8602-0.15750.3008
102.7793-0.73140.89593.46290.07132.6138-0.2813-0.73070.2362.0550.47090.2033-2.42930.27350.17431.6457-0.06490.05630.3776-0.17050.4094
112.7671-0.64820.38443.26140.73336.85690.81860.17720.17870.29960.80350.0558-2.2104-1.2883-0.24510.51270.310.20090.29370.16560.3296
Refinement TLS groupSelection details: chain C

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