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- PDB-2azo: DNA MISMATCH REPAIR PROTEIN MUTH FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 2azo
TitleDNA MISMATCH REPAIR PROTEIN MUTH FROM E. COLI
ComponentsMUTH
KeywordsENDONUCLEASE / MUTH / DNA REPAIR / HYDROLASE
Function / homology
Function and homology information


T/G mismatch-specific endonuclease activity / mismatch repair complex / regulation of DNA recombination / DNA modification / mismatch repair / endonuclease activity / DNA binding / cytoplasm
Similarity search - Function
DNA mismatch repair protein MutH / DNA mismatch repair MutH/Type II restriction enzyme Sau3AI / DNA mismatch repair enzyme MutH / DNA mismatch repair enzyme MutH / DNA mismatch repair MutH/Restriction endonuclease, type II / DNA mismatch repair MutH/Type II restriction endonuclease superfamily / ECO RV Endonuclease; Chain A / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA mismatch repair protein MutH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.3 Å
AuthorsYang, W.
CitationJournal: EMBO J. / Year: 1998
Title: Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases.
Authors: Ban, C. / Yang, W.
History
DepositionNov 20, 1997Processing site: BNL
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MUTH
B: MUTH


Theoretical massNumber of molelcules
Total (without water)51,6812
Polymers51,6812
Non-polymers00
Water2,594144
1
A: MUTH


Theoretical massNumber of molelcules
Total (without water)25,8411
Polymers25,8411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MUTH


Theoretical massNumber of molelcules
Total (without water)25,8411
Polymers25,8411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.860, 111.570, 54.930
Angle α, β, γ (deg.)90.00, 96.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.915447, -0.117429, 0.385006), (-0.091345, -0.992145, -0.085472), (0.392036, 0.043099, -0.91897)
Vector: -18.94685, 51.59971, 75.06109)
DetailsALTHOUGH THERE ARE TWO COPIES OF MUTH IN ONE ASYMMETRIC UNITS, THE COPIES ARE STRUCTURAL DIFFERENT DUE TO CONFORMATIONAL CHANGES BETWEEN TWO SUBDOMAINS IN THE PROTEIN.

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Components

#1: Protein MUTH / DNA MISMATCH REPAIR PROTEIN MUTH


Mass: 25840.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: PTX417 / Production host: Escherichia coli (E. coli) / References: UniProt: P06722
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.35 Å3/Da / Density % sol: 48 %
Crystal growpH: 6
Details: 100MM AMMONIUM ACETATE, 50 MM MAGNESIUM ACETATE, 1 MM DTT AND 12-16 % PEG6000, pH 6.0
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMammonium acetate1reservoir
250 mMmagnesium acetate1reservoir
31 mMdithiothreitol1reservoir
412-16 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 20757 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 10
Reflection shellResolution: 2.28→2.37 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2 / Rsym value: 0.369 / % possible all: 83.8
Reflection shell
*PLUS
% possible obs: 83.8 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1928 9.9 %RANDOM
Rwork0.202 ---
obs0.202 19388 91.6 %-
Displacement parametersBiso mean: 29.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 0 144 3652
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.421.5
X-RAY DIFFRACTIONx_mcangle_it3.912
X-RAY DIFFRACTIONx_scbond_it42
X-RAY DIFFRACTIONx_scangle_it6.12.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 302 10.8 %
Rwork0.3 2488 -
obs--79.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.225 / Rfactor Rfree: 0.289
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.399
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.65
LS refinement shell
*PLUS
Rfactor obs: 0.3

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