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- PDB-5b42: Crystal structure of the C-terminal endonuclease domain of Aquife... -

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Basic information

Entry
Database: PDB / ID: 5b42
TitleCrystal structure of the C-terminal endonuclease domain of Aquifex aeolicus MutL.
ComponentsDNA mismatch repair protein MutL
KeywordsDNA BINDING PROTEIN / mismatch repair / endonuclease / cadmium
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, dimerisation subdomain / DNA mismatch repair protein, MutL / 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 ...MutL, C-terminal domain, dimerisation subdomain / DNA mismatch repair protein, MutL / 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 / 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
: / DI(HYDROXYETHYL)ETHER / DNA mismatch repair protein MutL
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsFukui, K. / Baba, S. / Kumasaka, T. / Yano, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
the Ministry of Education, Science, Sports and Culture of Japan26850050 Japan
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Features and Functional Dependency on beta-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL
Authors: Fukui, K. / Baba, S. / Kumasaka, T. / Yano, T.
History
DepositionMar 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 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
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.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_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2399
Polymers12,3521
Non-polymers8878
Water1,71195
1
A: DNA mismatch repair protein MutL
hetero molecules

A: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,47818
Polymers24,7052
Non-polymers1,77316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5110 Å2
ΔGint-77 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.349, 35.349, 161.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein DNA mismatch repair protein MutL /


Mass: 12352.259 Da / Num. of mol.: 1 / Fragment: UNP residues 325-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: mutL, aq_1578 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: O67518
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 14.7mg/ml protein, 100mM sodium acetate, 50mM cadmium chloride, and 15%(v/v) polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→24.702 Å / Num. obs: 23801 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.821 / Rmerge(I) obs: 0.056 / Rsym value: 0.037 / Net I/σ(I): 59.8
Reflection shellResolution: 1.35→1.4 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→24.702 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.67
RfactorNum. reflection% reflection
Rfree0.1834 1139 5.15 %
Rwork0.14 --
obs0.1422 22100 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→24.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 20 95 976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011892
X-RAY DIFFRACTIONf_angle_d1.1681196
X-RAY DIFFRACTIONf_dihedral_angle_d22.682357
X-RAY DIFFRACTIONf_chiral_restr0.084125
X-RAY DIFFRACTIONf_plane_restr0.007152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3501-1.41150.25251470.14092740X-RAY DIFFRACTION100
1.4115-1.48590.19561470.14092730X-RAY DIFFRACTION100
1.4859-1.5790.19061670.13732713X-RAY DIFFRACTION100
1.579-1.70090.16791410.12242771X-RAY DIFFRACTION100
1.7009-1.8720.14091550.11782777X-RAY DIFFRACTION100
1.872-2.14280.17231480.11962786X-RAY DIFFRACTION100
2.1428-2.69920.17451300.14092503X-RAY DIFFRACTION88
2.6992-100.20571040.14091941X-RAY DIFFRACTION63

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