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- PDB-3gab: C-terminal domain of Bacillus subtilis MutL crystal form I -

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Basic information

Entry
Database: PDB / ID: 3gab
TitleC-terminal domain of Bacillus subtilis MutL crystal form I
ComponentsDNA mismatch repair protein mutL
KeywordsHYDROLASE / mismatch repair / endonuclease activity / DNA damage / DNA repair
Function / homology
Function and homology information


mismatch repair complex / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / ATP binding
Similarity search - Function
MutL, C-terminal domain, regulatory subdomain / MutL, C-terminal domain, dimerisation subdomain / DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / formyl-coa transferase, domain 3 / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain ...MutL, C-terminal domain, regulatory subdomain / MutL, C-terminal domain, dimerisation subdomain / DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / formyl-coa transferase, domain 3 / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / Ribosomal Protein S8; Chain: A, domain 1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA mismatch repair protein MutL
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsGuarne, A. / Pillon, M.C. / Lorenowicz, J.J. / Mitchell, R.R. / Chung, Y.S. / Friedhoff, P.
CitationJournal: Mol.Cell / Year: 2010
Title: Structure of the endonuclease domain of MutL: unlicensed to cut.
Authors: Pillon, M.C. / Lorenowicz, J.J. / Uckelmann, M. / Klocko, A.D. / Mitchell, R.R. / Chung, Y.S. / Modrich, P. / Walker, G.C. / Simmons, L.A. / Friedhoff, P. / Guarne, A.
History
DepositionFeb 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA mismatch repair protein mutL
B: DNA mismatch repair protein mutL
C: DNA mismatch repair protein mutL
D: DNA mismatch repair protein mutL


Theoretical massNumber of molelcules
Total (without water)91,4694
Polymers91,4694
Non-polymers00
Water1,820101
1
A: DNA mismatch repair protein mutL

A: DNA mismatch repair protein mutL


Theoretical massNumber of molelcules
Total (without water)45,7342
Polymers45,7342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2160 Å2
ΔGint-26 kcal/mol
Surface area19240 Å2
MethodPISA
2
B: DNA mismatch repair protein mutL
C: DNA mismatch repair protein mutL


Theoretical massNumber of molelcules
Total (without water)45,7342
Polymers45,7342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-25 kcal/mol
Surface area19090 Å2
MethodPISA
3
D: DNA mismatch repair protein mutL

D: DNA mismatch repair protein mutL


Theoretical massNumber of molelcules
Total (without water)45,7342
Polymers45,7342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2080 Å2
ΔGint-25 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.288, 94.894, 218.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
DNA mismatch repair protein mutL


Mass: 22867.223 Da / Num. of mol.: 4 / Fragment: residues 434-627
Source method: isolated from a genetically manipulated source
Details: cloned using NcoI and XhoI restriction sites / Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU17050, mutL / Plasmid: pProEXHta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) STAR / References: UniProt: P49850
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 24-29% PEG MME 550, 0.1 M MgCl2, 0.1 M TRIS pH 9, 5% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9792, 0.9794, 0.9686
SYNCHROTRONNSLS X29A21.0809
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDOct 27, 2007mirrors
ADSC QUANTUM 3152CCDApr 24, 2008mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111MADMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.96861
41.08091
ReflectionResolution: 2.38→50 Å / Num. all: 37176 / Num. obs: 35660 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.034 / Net I/σ(I): 41.5
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2768 / Rsym value: 0.194 / % possible all: 76

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.778 Å / SU ML: 0.02 / σ(F): 1.34 / σ(I): 0 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 1631 5.13 %
Rwork0.2164 --
obs0.2189 31771 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.57 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 136.4 Å2 / Biso mean: 54.988 Å2 / Biso min: 18.99 Å2
Baniso -1Baniso -2Baniso -3
1-2.979 Å20 Å2-0 Å2
2--0.872 Å2-0 Å2
3----3.851 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6015 0 0 101 6116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036153
X-RAY DIFFRACTIONf_angle_d0.6098299
X-RAY DIFFRACTIONf_chiral_restr0.041896
X-RAY DIFFRACTIONf_plane_restr0.0031078
X-RAY DIFFRACTIONf_dihedral_angle_d15.5212321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5-2.57360.31831530.25142266241993
2.5736-2.65660.2761280.24672449257798
2.6566-2.75150.34711260.24762516264299
2.7515-2.86160.32131280.252225002628100
2.8616-2.99170.36011390.273625162655100
2.9917-3.14920.31861340.28325052639100
3.1492-3.34630.34281550.251124932648100
3.3463-3.60430.26651410.222825552696100
3.6043-3.96620.23071320.196725292661100
3.9662-4.53840.22251320.175325682700100
4.5384-5.71130.22451390.180425722711100
5.7113-29.780.22651240.19252671279598

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