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

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Basic information

Entry
Database: PDB / ID: 3mip
TitleI-MsoI re-designed for altered DNA cleavage specificity (-8GCG)
Components
  • DNA (5'-D(*CP*GP*GP*AP*GP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*GP*CP*CP*TP*GP*C)-3')
  • DNA (5'-D(*GP*CP*AP*GP*GP*CP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*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: 2.4 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 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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*CP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*CP*TP*CP*CP*G)-3')
D: DNA (5'-D(*CP*GP*GP*AP*GP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*GP*CP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2937
Polymers52,1734
Non-polymers1203
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint-88 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.539, 42.611, 71.524
Angle α, β, γ (deg.)96.45, 107.04, 108.56
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 6:166 )
211chain B and (resseq 6:166 )

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Components

#1: Protein Mso-8G


Mass: 18713.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / 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*CP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*CP*TP*CP*CP*G)-3')


Mass: 7412.753 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*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*GP*CP*CP*TP*GP*C)-3')


Mass: 7332.705 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 / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 20% PEG 4000, 100mM Tris, 20mM NaCl, 5mM CaCl2, pH 7.8, 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 SATURN 944+ / Detector: CCD / Date: Aug 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: 2.4→30 Å / Num. all: 17948 / Num. obs: 17356 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.054
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 5.6 / Num. unique all: 1675 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→22.959 Å / SU ML: 0.37 / σ(F): 0.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2855 1582 10.03 %random
Rwork0.2257 ---
obs0.2316 15769 90.9 %-
all-17351 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.973 Å2 / ksol: 0.316 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→22.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 978 3 87 3712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063790
X-RAY DIFFRACTIONf_angle_d1.1845318
X-RAY DIFFRACTIONf_dihedral_angle_d23.1811510
X-RAY DIFFRACTIONf_chiral_restr0.061586
X-RAY DIFFRACTIONf_plane_restr0.004516
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1322X-RAY DIFFRACTIONPOSITIONAL
12B1322X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4750.33761260.28521168X-RAY DIFFRACTION82
2.475-2.56330.35041380.29811187X-RAY DIFFRACTION86
2.5633-2.66580.32961410.28911255X-RAY DIFFRACTION87
2.6658-2.78690.34681330.30471195X-RAY DIFFRACTION86
2.7869-2.93360.39081400.29821243X-RAY DIFFRACTION87
2.9336-3.11690.35671440.27311294X-RAY DIFFRACTION90
3.1169-3.35690.26841490.23651320X-RAY DIFFRACTION94
3.3569-3.69350.26871530.21481375X-RAY DIFFRACTION97
3.6935-4.22510.25931540.20471382X-RAY DIFFRACTION96
4.2251-5.31220.2451460.15811387X-RAY DIFFRACTION97
5.3122-22.95990.20231580.171381X-RAY DIFFRACTION98
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
1refined-0.04540.1304-0.28450.54660.01541.2547-0.09860.3187-0.1741-0.2350.2104-0.2560.61330.3061-0.17760.1794-0.0048-0.05590.1668-0.01680.23124.6726-2.6558-1.3208
20.2461-0.02710.04220.2020.1014-0.01630.09140.09840.0877-0.01960.0634-0.06920.0084-0.1679-0.07130.544-0.09890.07120.4722-0.05950.3251
3-0.0557-0.413-0.61380.36280.05890.6949-0.2235-0.25160.0429-0.28510.3472-0.07250.89780.4839-0.1363-0.49770.2528-0.35960.1549-0.0053-0.0394
4-0.170.0104-0.12360.28140.09020.40760.13230.1396-0.031-0.14190.12150.0137-0.0372-0.0809-0.13940.12420.0424-0.08080.41720.11120.2108
50.1615-0.22440.07810.2672-0.24890.33870.06640.11640.1348-0.03250.2465-0.125-0.3901-0.0957-0.18020.4398-0.02360.06710.14140.05910.2211
60.10570.4674-0.36640.51810.07580.63710.1022-0.10280.10450.3696-0.09990.2744-0.0603-0.487-0.09120.1921-0.0034-0.02070.20340.03790.2173
70.1388-0.0181-0.0810.0969-0.08720.01620.0842-0.0751-0.0122-0.01390.1665-0.04320.12240.0508-0.10090.5365-0.04180.03590.5465-0.09050.3978
80.9188-0.0073-0.14680.39730.16341.68040.4281-0.00120.01450.1736-0.08730.0617-0.4156-0.5011-0.21080.15450.12440.01910.14990.09670.1354
90.3202-0.19460.15790.1513-0.10660.36760.1325-0.1815-0.10690.06540.1867-0.06340.03960.0795-0.13930.29610.0883-0.1070.22320.03780.2166
100.5643-0.04490.43350.42090.23470.25630.20230.22720.06210.23960.1437-0.08980.10730.3766-0.33860.2383-0.0898-0.05030.3963-0.06560.2335
110.5160.28831.00560.6185-0.99392.34910.33050.0470.151-0.00910.3657-0.0291-1.12430.7128-0.51620.4065-0.22970.17520.2271-0.13770.2417
Refinement TLS groupSelection details: chain C

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