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- PDB-5akb: MutS in complex with the N-terminal domain of MutL - crystal form 1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5akb | ||||||
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Title | MutS in complex with the N-terminal domain of MutL - crystal form 1 | ||||||
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![]() | DNA BINDING PROTEIN / HYDROLASE / DNA MISMATCH REPAIR / COMPLEX / SLIDING CLAMP / CROSSLINKING | ||||||
Function / homology | ![]() single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity ...single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding / DNA damage response / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Groothuizen, F.S. / Winkler, I. / Cristovao, M. / Fish, A. / Winterwerp, H.H.K. / Reumer, A. / Marx, A.D. / Hermans, N. / Nicholls, R.A. / Murshudov, G.N. ...Groothuizen, F.S. / Winkler, I. / Cristovao, M. / Fish, A. / Winterwerp, H.H.K. / Reumer, A. / Marx, A.D. / Hermans, N. / Nicholls, R.A. / Murshudov, G.N. / Lebbink, J.H.G. / Friedhoff, P. / Sixma, T.K. | ||||||
![]() | ![]() Title: MutS/MutL crystal structure reveals that the MutS sliding clamp loads MutL onto DNA. Authors: Groothuizen, F.S. / Winkler, I. / Cristovao, M. / Fish, A. / Winterwerp, H.H. / Reumer, A. / Marx, A.D. / Hermans, N. / Nicholls, R.A. / Murshudov, G.N. / Lebbink, J.H. / Friedhoff, P. / Sixma, T.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 944.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5akcC ![]() 5akdC ![]() 1bknS ![]() 1w7aS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Details | IN THIS STRUCTURE SINGLE CYSTEINES IN MUTS AND THE LN40 DOMAIN OF MUTL HAVE BEEN PLACED SUCH THAT CROSSLINKING OCCURS ONLY IN THE PRESENCE OF A DNA MISMATCH AND A NUCLEOTIDE (SEE WINKLER ET AL 2011, JBC). TO OBTAIN HOMOGENEOUS MATERIAL BOTH MUTS SUBUNITS HAVE BEEN CROSSLINKED TO A MUTL(LN40), WHEREAS FOR BIOLOGICAL FUNCTION ONLY ONE MUTL PER MUTS DIMER IS REQUIRED. |
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Components
#1: Protein | Mass: 89476.086 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Details: BM(PEO)3 (THIOETHER) CROSSLINK BETWEEN-A 246 AND D 131, B 246 AND C 131, E 246 AND F 131 Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 41275.738 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | Sequence details | NATIVE CYSTEINES REPLACED AND ONE CYSTEINE INTRODUCED N-TERMINAL HIS-TAG. NATIVE CYSTEINES REPLACED ...NATIVE CYSTEINES REPLACED AND ONE CYSTEINE INTRODUCED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 70 % / Description: NONE |
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Crystal grow | Details: 9-12% PEG8000, 100 MM TRIS PH 7.0, 200 MM MGCL2, 80-450 MM SODIUM MALONATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 4.71→82.7 Å / Num. obs: 31052 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 2.5 |
Reflection shell | Resolution: 4.71→4.96 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1W7A AND 1BKN Resolution: 4.71→199.73 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.87 / SU B: 586.437 / SU ML: 2.651 / Cross valid method: THROUGHOUT / ESU R Free: 1.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES WITH TLS ADDED RESIDUES ABE1-127, ABE660-669, E442-516, CDF1-19, CDF74-79, CDF126-131, CDF300-314, CDF332-349 ARE DISORDERED. CROSSLINKER BMPEO3 IS DISORDERED. IN THIS STRUCTURE ...Details: U VALUES WITH TLS ADDED RESIDUES ABE1-127, ABE660-669, E442-516, CDF1-19, CDF74-79, CDF126-131, CDF300-314, CDF332-349 ARE DISORDERED. CROSSLINKER BMPEO3 IS DISORDERED. IN THIS STRUCTURE SINGLE CYSTEINES IN MUTS AND THE LN40 DOMAIN OF MUTL HAVE BEEN PLACED SUCH THAT CROSSLINKING OCCURS ONLY IN THE PRESENCE OF A DNA MISMATCH AND A NUCLEOTIDE (SEE WINKLER ET AL 2011, JBC). TO OBTAIN HOMOGENEOUS MATERIAL BOTH MUTS SUBUNIT HAVE BEEN CROSSLINKED TO A MUTL(LN40), WHEREAS FOR BIOLOGICAL FUNCTION ONLY ONE MUTL PER MUTS DIMER IS REQUIRED.
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Solvent computation | Ion probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 234.958 Å2
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Refinement step | Cycle: LAST / Resolution: 4.71→199.73 Å
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Refine LS restraints |
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