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- PDB-6lzk: Aquifex aeolicus MutL ATPase domain with K252N mutation -

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Basic information

Entry
Database: PDB / ID: 6lzk
TitleAquifex aeolicus MutL ATPase domain with K252N mutation
ComponentsDNA mismatch repair protein MutL
KeywordsDNA BINDING PROTEIN / DNA repair / ATPase
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
DNA mismatch repair protein, MutL / 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 protein, MutL / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DNA mismatch repair protein MutL
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1594962224 Å
AuthorsFukui, K. / Izuhara, K. / Yano, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K07376 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A Lynch syndrome-associated mutation at a Bergerat ATP-binding fold destabilizes the structure of the DNA mismatch repair endonuclease MutL.
Authors: Izuhara, K. / Fukui, K. / Murakawa, T. / Baba, S. / Kumasaka, T. / Uchiyama, K. / Yano, T.
History
DepositionFeb 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2037
Polymers106,9453
Non-polymers2584
Water905
1
A: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9075
Polymers35,6481
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-11 kcal/mol
Surface area13610 Å2
MethodPISA
2
B: DNA mismatch repair protein MutL


Theoretical massNumber of molelcules
Total (without water)35,6481
Polymers35,6481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13530 Å2
MethodPISA
3
C: DNA mismatch repair protein MutL


Theoretical massNumber of molelcules
Total (without water)35,6481
Polymers35,6481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.900, 146.295, 175.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLYSLYS(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA12 - 4112 - 41
12ARGARGGLUGLU(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA45 - 6245 - 62
13VALVALLEULEU(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA64 - 6664 - 66
14TYRTYRLEULEU(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA93 - 10393 - 103
15SERSERPHEPHE(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA105 - 108105 - 108
16GLUGLUGLUGLU(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA110110
17GLYGLYARGARG(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA113 - 127113 - 127
18VALVALLYSLYS(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA129 - 154129 - 154
19GLUGLUVALVAL(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA156 - 177156 - 177
110PHEPHEARGARG(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA179 - 186179 - 186
111LEULEULEULEU(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA191 - 196191 - 196
112ARGARGTHRTHR(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA199 - 208199 - 208
113GLUGLUARGARG(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA210 - 226210 - 226
114TYRTYRASNASN(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA233 - 238233 - 238
115PROPROILEILE(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA241 - 242241 - 242
116ASNASNARGARG(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA246 - 252246 - 252
117VALVALTYRTYR(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA254 - 257254 - 257
118THRTHRPROPRO(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA259 - 269259 - 269
119VALVALVALVAL(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA272272
120VALVALLEULEU(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA283 - 286283 - 286
121GLUGLUGLUGLU(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA288288
122LYSLYSLEULEU(chain A and (resseq 12:41 or resseq 45:62 or resseq...AA290 - 298290 - 298
21VALVALLYSLYS(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB12 - 4112 - 41
22ARGARGGLUGLU(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB45 - 6245 - 62
23VALVALLEULEU(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB64 - 6664 - 66
24TYRTYRLEULEU(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB93 - 10393 - 103
25SERSERPHEPHE(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB105 - 108105 - 108
26GLUGLUGLUGLU(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB110110
27GLYGLYARGARG(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB113 - 127113 - 127
28VALVALLYSLYS(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB129 - 154129 - 154
29GLUGLUVALVAL(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB156 - 177156 - 177
210PHEPHEARGARG(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB179 - 186179 - 186
211LEULEULEULEU(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB191 - 196191 - 196
212ARGARGTHRTHR(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB199 - 208199 - 208
213GLUGLUARGARG(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB210 - 226210 - 226
214TYRTYRASNASN(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB233 - 238233 - 238
215PROPROILEILE(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB241 - 242241 - 242
216ASNASNARGARG(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB246 - 252246 - 252
217VALVALTYRTYR(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB254 - 257254 - 257
218THRTHRPROPRO(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB259 - 269259 - 269
219VALVALVALVAL(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB272272
220VALVALLEULEU(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB283 - 286283 - 286
221GLUGLUGLUGLU(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB288288
222LYSLYSLEULEU(chain B and (resseq 12:41 or resseq 45:62 or resseq...BB290 - 298290 - 298
31VALVALLYSLYS(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC12 - 4112 - 41
32ARGARGGLUGLU(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC45 - 6245 - 62
33VALVALLEULEU(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC64 - 6664 - 66
34TYRTYRLEULEU(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC93 - 10393 - 103
35SERSERPHEPHE(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC105 - 108105 - 108
36GLUGLUGLUGLU(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC110110
37GLYGLYARGARG(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC113 - 127113 - 127
38VALVALLYSLYS(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC129 - 154129 - 154
39GLUGLUVALVAL(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC156 - 177156 - 177
310PHEPHEARGARG(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC179 - 186179 - 186
311LEULEULEULEU(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC191 - 196191 - 196
312ARGARGTHRTHR(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC199 - 208199 - 208
313GLUGLUARGARG(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC210 - 226210 - 226
314TYRTYRASNASN(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC233 - 238233 - 238
315PROPROILEILE(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC241 - 242241 - 242
316ASNASNARGARG(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC246 - 252246 - 252
317VALVALTYRTYR(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC254 - 257254 - 257
318THRTHRPROPRO(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC259 - 269259 - 269
319VALVALVALVAL(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC272272
320VALVALLEULEU(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC283 - 286283 - 286
321GLUGLUGLUGLU(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC288288
322LYSLYSLEULEU(chain C and (resseq 12:41 or resseq 45:62 or resseq...CC290 - 298290 - 298

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Components

#1: Protein DNA mismatch repair protein MutL /


Mass: 35648.344 Da / Num. of mol.: 3 / Mutation: K252N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: mutL / Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: O67518
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.87 Å3/Da / Density % sol: 68.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 2.5 M NaCl, 100 mM KH2PO4/Na2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.159→50 Å / Num. obs: 26577 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 80.4551785757 Å2 / CC1/2: 0.793 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.041 / Net I/σ(I): 23.4
Reflection shellResolution: 3.159→3.31 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 2.59 / Num. unique obs: 2579 / Rpim(I) all: 0.356 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data processing
PHENIXv1.10.1refinement
HKL-2000data scaling
PHENIXv1.10.1phasing
PHENIXv1.10.1model building
Cootv0.7.2model building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5x9y

5x9y


Resolution: 3.1594962224→42.3567969143 Å / SU ML: 0.396478435291 / Cross valid method: FREE R-VALUE / σ(F): 0.000377438832797 / Phase error: 26.1382003729
RfactorNum. reflection% reflection
Rfree0.27175280184 1832 6.89317831207 %
Rwork0.228393923339 --
obs0.231393173265 26577 92.2524211184 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 96.3299241187 Å2
Refinement stepCycle: LAST / Resolution: 3.1594962224→42.3567969143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6020 0 16 5 6041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048843799246108
X-RAY DIFFRACTIONf_angle_d0.9917688712148167
X-RAY DIFFRACTIONf_chiral_restr0.0582487687399936
X-RAY DIFFRACTIONf_plane_restr0.00516657863571028
X-RAY DIFFRACTIONf_dihedral_angle_d13.71652143483806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1595-3.24490.3277881341841120.2423331328341539X-RAY DIFFRACTION76.0479041916
3.2449-3.34030.2982960519071260.2277016402531713X-RAY DIFFRACTION83.8577291382
3.3403-3.44810.2222998863051290.1967141091771774X-RAY DIFFRACTION86.5393360618
3.4481-3.57130.27622915561360.212092631271839X-RAY DIFFRACTION90.7628676471
3.5713-3.71420.258958735871430.2253064902271905X-RAY DIFFRACTION93.4306569343
3.7142-3.88310.2747703796581390.2409402911441903X-RAY DIFFRACTION92.8181818182
3.8831-4.08770.2812170155931420.2403453105081926X-RAY DIFFRACTION93.321299639
4.0877-4.34360.2703338760931380.211778989271933X-RAY DIFFRACTION94.8694457169
4.3436-4.67850.2370446360731490.1936095870861980X-RAY DIFFRACTION96.0740072202
4.6785-5.14860.242578081961500.2058225506931986X-RAY DIFFRACTION96.6078697422
5.1486-5.89190.2995187917341510.2479964135342031X-RAY DIFFRACTION97.3672467648
5.8919-7.41670.3086312175691550.2655258275822058X-RAY DIFFRACTION98.1374722838
7.4167-8.810.2723165343211620.2376545090342158X-RAY DIFFRACTION98.5975350616
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.2430964840460.06335767331690.4059416997950.605056016937-0.2252088348460.8365977466870.09466427320330.002142097214280.129606725275-0.014297235035-0.1070616565070.1370270397350.1325318044370.0422646908847-5.95452161153E-50.4796656956430.0111125925430.03483492099190.283896920398-0.01680204669070.475189564207-5.8565864525917.448509791337.3002273262
20.445424224267-0.417032207648-0.09812051209520.477110463837-0.1835653897211.029500570930.01567138094040.9107507924050.04023207936840.1023815105010.07648689525370.01194391311840.07723607257940.5944130687020.001863321915710.7118354181380.140907901101-0.1844113299280.9854703781470.1108046054710.533521614282-14.68656858046.48851359204-8.81132955082
30.931946404585-0.138144492669-0.07788597175230.5449734827030.1576173649770.0518622599225-0.08590947705030.6752629181350.428395373662-0.180020922479-0.06695071001470.00869792961517-0.26954034316-0.9258591280390.04851889101610.2718590064170.15639743103-0.2251846242911.31176673548-0.210606195930.648339258722-36.129109249137.808930514227.7981852962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 12:301)
2X-RAY DIFFRACTION2(chain B and resseq 12:301)
3X-RAY DIFFRACTION3(chain C and resseq 12:298)

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