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- PDB-5z42: Aquifex aeolicus MutL endonuclease domain with three zinc ions. -

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Basic information

Entry
Database: PDB / ID: 5z42
TitleAquifex aeolicus MutL endonuclease domain with three zinc ions.
ComponentsDNA mismatch repair protein MutL
KeywordsDNA BINDING PROTEIN / mismatch repair protein / endonuclease / zinc / thermophile
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: 1.3 Å
AuthorsFukui, K. / Yano, T.
CitationJournal: FEBS Lett. / Year: 2018
Title: Multiple zinc ions maintain the open conformation of the catalytic site in the DNA mismatch repair endonuclease MutL from Aquifex aeolicus
Authors: Fukui, K. / Baba, S. / Kumasaka, T. / Yano, T.
History
DepositionJan 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 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)12,89111
Polymers12,3521
Non-polymers53910
Water2,324129
1
A: DNA mismatch repair protein MutL
hetero molecules

A: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,78222
Polymers24,7052
Non-polymers1,07820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5000 Å2
ΔGint-372 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.623, 35.623, 167.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#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 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: O67518

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Non-polymers , 6 types, 139 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100mM sodium acetate, 5mM zinc acetate, 15%(v/v) polyethylene glycol 400, pH 4.6

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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: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 27699 / % possible obs: 98.9 % / Redundancy: 13.6 % / CC1/2: 0.978 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.077 / Net I/σ(I): 50.7
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 14 % / Rmerge(I) obs: 0.828 / Mean I/σ(I) obs: 3.333 / Num. unique obs: 1360 / CC1/2: 0.978 / Rpim(I) all: 0.226 / Rrim(I) all: 0.859 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.3→32.793 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.64
RfactorNum. reflection% reflection
Rfree0.2041 1999 7.23 %
Rwork0.1894 --
obs0.1905 27636 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→32.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms869 0 16 129 1014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013894
X-RAY DIFFRACTIONf_angle_d1.2711201
X-RAY DIFFRACTIONf_dihedral_angle_d21.686357
X-RAY DIFFRACTIONf_chiral_restr0.095126
X-RAY DIFFRACTIONf_plane_restr0.009153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2998-1.33230.23351380.23191766X-RAY DIFFRACTION98
1.3323-1.36830.21971380.21911780X-RAY DIFFRACTION98
1.3683-1.40860.21911380.20961760X-RAY DIFFRACTION98
1.4086-1.4540.28411370.20271763X-RAY DIFFRACTION99
1.454-1.5060.22621410.18541797X-RAY DIFFRACTION99
1.506-1.56630.18571400.17451802X-RAY DIFFRACTION99
1.5663-1.63760.21981410.16741795X-RAY DIFFRACTION99
1.6376-1.72390.21451410.17591810X-RAY DIFFRACTION99
1.7239-1.83190.19591410.17931811X-RAY DIFFRACTION99
1.8319-1.97330.21341450.17381868X-RAY DIFFRACTION100
1.9733-2.17190.19851450.17331843X-RAY DIFFRACTION100
2.1719-2.48610.20291450.18651875X-RAY DIFFRACTION100
2.4861-3.13180.21051500.20781919X-RAY DIFFRACTION100
3.1318-32.80370.18921590.19182048X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 16.9063 Å / Origin y: 6.7123 Å / Origin z: -10.0108 Å
111213212223313233
T0.1054 Å20.0144 Å2-0.0186 Å2-0.1221 Å20.0033 Å2--0.1257 Å2
L0.3819 °20.2562 °2-0.1185 °2-0.7822 °20.5786 °2--2.356 °2
S-0.0039 Å °0.0171 Å °0.0042 Å °-0.0183 Å °0.0479 Å °-0.057 Å °-0.0257 Å °0.2005 Å °-0.0372 Å °
Refinement TLS groupSelection details: all

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