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- PDB-3kdk: Structure of the C-terminal domain of Bacillus subtilis MutL boun... -

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Basic information

Entry
Database: PDB / ID: 3kdk
TitleStructure of the C-terminal domain of Bacillus subtilis MutL bound to Zn2+
ComponentsDNA mismatch repair protein mutL
KeywordsHYDROLASE / mismatch repair / MutL / endonuclease / Zn-binding protein / 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 / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsGuarne, A. / Pillon, M.C.
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
DepositionOct 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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_ref_seq_dif / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _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: DNA mismatch repair protein mutL
B: DNA mismatch repair protein mutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9966
Polymers45,7342
Non-polymers2624
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-25 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.231, 74.608, 182.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA mismatch repair protein mutL /


Mass: 22867.223 Da / Num. of mol.: 2 / Fragment: residues 434-627
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU17050, mutL / Plasmid: pProEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P49850
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 25% PEG 3350, 0.2 M NaCl, 0.1 mM ZnCl2, 0.1 M TRIS pH 7.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.2796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2796 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 41093 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.067 / Net I/σ(I): 20.8
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.494 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GAB

3gab


Resolution: 2.26→32.75 Å / SU ML: 0.34 / σ(F): 1.89 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 2113 5.15 %
Rwork0.2141 --
obs0.2169 41004 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.938 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 64.733 Å2
Baniso -1Baniso -2Baniso -3
1-1.404 Å20 Å2-0 Å2
2--3.826 Å2-0 Å2
3----5.229 Å2
Refinement stepCycle: LAST / Resolution: 2.26→32.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 4 74 3114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043109
X-RAY DIFFRACTIONf_angle_d0.7454192
X-RAY DIFFRACTIONf_dihedral_angle_d17.3311180
X-RAY DIFFRACTIONf_chiral_restr0.051451
X-RAY DIFFRACTIONf_plane_restr0.003545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.33670.3512120.27133810X-RAY DIFFRACTION97
2.3367-2.43020.3162240.25463856X-RAY DIFFRACTION100
2.4302-2.54080.31332260.24713943X-RAY DIFFRACTION100
2.5408-2.67470.32241960.23483849X-RAY DIFFRACTION100
2.6747-2.84220.25822490.22323911X-RAY DIFFRACTION100
2.8422-3.06140.28942110.233906X-RAY DIFFRACTION100
3.0614-3.36930.30051890.22423930X-RAY DIFFRACTION100
3.3693-3.85610.25871960.2013912X-RAY DIFFRACTION100
3.8561-4.85580.23342200.17683900X-RAY DIFFRACTION100
4.8558-32.7530.21381900.18983874X-RAY DIFFRACTION98
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)
1refined0.76610.4523-0.35770.4257-0.17550.60310.02290.0551-0.0544-0.04350.082-0.0008-0.29630.362800.2572-0.03760.02020.2244-0.01890.1945-1.4839-5.91811.1181
21.72840.611-0.05011.6681-0.080.96420.8060.41710.3023-0.3687-0.7139-0.0807-0.69240.4522-0.00050.86360.05540.21740.62420.10440.1489
30.88571.2414-0.46451.6917-0.65381.9466-0.0652-0.1159-0.06150.5833-0.0887-0.0944-0.84820.6651-0.07750.1502-0.05610.00420.2092-0.02170.1872
40.365-0.043-0.2821.2606-0.81570.7437-0.0340.0476-0.06690.1263-0.08620.1204-0.08550.04240.00010.2066-0.04160.06310.1316-0.00070.2272
54.0115-0.4765-1.48931.3860.25992.11910.2393-0.83460.13380.0568-0.1585-0.06840.00440.2102-0.00010.1741-0.1095-0.02630.3734-0.00840.1956
61.3310.95230.34941.2846-0.1861.27820.0586-0.0177-0.02430.00420.07970.17340.35790.08830.00010.25040.09180.08180.1442-0.00030.304
Refinement TLS groupSelection details: chain B and resid 581:624

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