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- PDB-3zlj: CRYSTAL STRUCTURE OF FULL-LENGTH E.COLI DNA MISMATCH REPAIR PROTE... -

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Basic information

Entry
Database: PDB / ID: 3zlj
TitleCRYSTAL STRUCTURE OF FULL-LENGTH E.COLI DNA MISMATCH REPAIR PROTEIN MUTS D835R MUTANT IN COMPLEX WITH GT MISMATCHED DNA
Components
  • (DNA MISMATCH REPAIR PROTEIN MUTS) x 2
  • 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*CP*AP*CP*CP *AP*GP*TP*GP*TP*CP*AP)-3'
  • 5'-D(*TP*GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*TP*TP *GP*GP*CP*AP*GP*CP*TP)-3'
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX / DIMER MUTANT / MISMATCH REPAIR / DNA REPAIR PROTEIN / DNA DAMAGE / NUCLEOTIDE-BINDING / ATP-BINDING
Function / homology
Function and homology information


adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding ...adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
MutS, connector domain / DNA repair protein MutS, domain I / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / DNA mismatch repair protein MutS / DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal ...MutS, connector domain / DNA repair protein MutS, domain I / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / DNA mismatch repair protein MutS / DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV / MutS domain III / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / MutS, DNA mismatch repair protein, domain I / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGroothuizen, F.S. / Fish, A. / Petoukhov, M.V. / Reumer, A. / Manelyte, L. / Winterwerp, H.H.K. / Marinus, M.G. / Lebbink, J.H.G. / Svergun, D.I. / Friedhoff, P. / Sixma, T.K.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Using Stable Muts Dimers and Tetramers to Quantitatively Analyze DNA Mismatch Recognition and Sliding Clamp Formation.
Authors: Groothuizen, F.S. / Fish, A. / Petoukhov, M.V. / Reumer, A. / Manelyte, L. / Winterwerp, H.H.K. / Marinus, M.G. / Lebbink, J.H.G. / Svergun, D.I. / Friedhoff, P. / Sixma, T.K.
History
DepositionFeb 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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 MUTS
B: DNA MISMATCH REPAIR PROTEIN MUTS
C: DNA MISMATCH REPAIR PROTEIN MUTS
D: DNA MISMATCH REPAIR PROTEIN MUTS
E: 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*CP*AP*CP*CP *AP*GP*TP*GP*TP*CP*AP)-3'
F: 5'-D(*TP*GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*TP*TP *GP*GP*CP*AP*GP*CP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)203,7356
Polymers203,7356
Non-polymers00
Water0
1
A: DNA MISMATCH REPAIR PROTEIN MUTS
B: DNA MISMATCH REPAIR PROTEIN MUTS
E: 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*CP*AP*CP*CP *AP*GP*TP*GP*TP*CP*AP)-3'
F: 5'-D(*TP*GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*TP*TP *GP*GP*CP*AP*GP*CP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)192,1124
Polymers192,1124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-70.2 kcal/mol
Surface area69490 Å2
MethodPISA
2
C: DNA MISMATCH REPAIR PROTEIN MUTS
D: DNA MISMATCH REPAIR PROTEIN MUTS


Theoretical massNumber of molelcules
Total (without water)11,6232
Polymers11,6232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-19.6 kcal/mol
Surface area4670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.288, 91.152, 112.855
Angle α, β, γ (deg.)90.00, 101.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUILEILEAA26 - 79926 - 799
21GLUGLUILEILEBB26 - 79926 - 799
12SERSERVALVALCC823 - 85323 - 53
22SERSERVALVALDD823 - 85323 - 53

NCS ensembles :
ID
1
2

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Components

#1: Protein DNA MISMATCH REPAIR PROTEIN MUTS /


Mass: 89604.359 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / Variant (production host): PLYSS / References: UniProt: P23909
#2: Protein DNA MISMATCH REPAIR PROTEIN MUTS /


Mass: 5811.530 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CHAINS C AND D ARE THE C-TERMINAL PORTION OF CHAINS A AND B, HOWEVER THE MISSING REGION 800-822 MAKES UNAMBIGUOUS ASSIGNMENT TO THE CORRECT CHAIN IMPOSSIBLE
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / Variant (production host): PLYSS / References: UniProt: P23909
#3: DNA chain 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*CP*AP*CP*CP *AP*GP*TP*GP*TP*CP*AP)-3'


Mass: 6433.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*TP*GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*TP*TP *GP*GP*CP*AP*GP*CP*TP)-3'


Mass: 6470.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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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: 2.72 Å3/Da / Density % sol: 59.7 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5MM TRIS PH8, 750MM NACL, 12% PEG 6000, 10MM MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.1→47.24 Å / Num. obs: 40031 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.9
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E3M

1e3m


Resolution: 3.1→46.49 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.884 / SU B: 49.479 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.49 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26283 2006 5 %RANDOM
Rwork0.22734 ---
obs0.22912 37981 99.84 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.792 Å2
Baniso -1Baniso -2Baniso -3
1-3.55 Å20 Å2-0.71 Å2
2---4.3 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 3.1→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12499 734 0 0 13233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01913527
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212824
X-RAY DIFFRACTIONr_angle_refined_deg1.0021.92418463
X-RAY DIFFRACTIONr_angle_other_deg0.919329418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.01151575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73523.471605
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.262152266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.19215131
X-RAY DIFFRACTIONr_chiral_restr0.0540.22067
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02114800
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023063
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A439890.12
12B439890.12
21C13650.2
22D13650.2
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 156 -
Rwork0.31 2790 -
obs--100 %
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)
12.77220.0090.64791.75770.52234.0585-0.01330.05130.2990.09350.14570.3649-0.4976-0.037-0.13240.32930.02070.0120.1741-0.01240.2959-34.214640.2064-15.3162
22.89590.84280.54363.8686-0.79794.16330.2265-0.1954-0.17070.2851-0.04590.1518-0.10150.0738-0.18050.07730.00990.02660.1128-0.02620.124-23.67615.1968-2.8096
33.9778-1.6151.08271.0363-0.92761.99480.20250.2859-0.2719-0.2612-0.03370.37560.2761-0.0744-0.16880.2318-0.0584-0.07070.1876-0.04990.3205-31.83313.0839-22.8611
44.79721.73531.26134.3179-0.35275.8192-0.16870.1713-0.0589-0.85460.12980.54360.0511-0.47010.0390.52970.0532-0.29430.5155-0.0960.5338-59.592439.5033-50.4545
50.71070.36920.39590.5646-0.42682.22260.09990.1538-0.0904-0.03540.26470.36550.2766-0.253-0.36460.0635-0.0904-0.02480.30650.04960.6441-39.11677.2112-23.0204
64.97330.85741.76682.08550.94761.8860.10170.3822-0.1776-0.1712-0.0539-0.3559-0.18810.2377-0.04780.24170.06960.12270.20010.03530.19695.2443-4.3576-11.4122
73.1057-0.89120.29592.7228-5.329413.27780.1465-0.3248-0.3578-0.017-0.0125-0.24060.36550.5924-0.13410.50660.04710.22180.2698-0.17250.818331.19033.4852-21.7749
85.2977-1.1278-0.89180.30970.17440.1642-0.09870.3606-0.34310.35430.0086-0.0139-0.0275-0.17660.09011.57260.0045-0.46451.10660.0491.0793-15.702728.4125-42.6905
94.9864-3.1258-0.37594.3907-1.04343.69120.84711.0308-0.6573-1.3813-0.58580.21580.6150.1919-0.26121.09280.1346-0.07790.4778-0.16260.22969.905331.4544-47.5947
102.6634-2.20361.79113.2591-1.63381.61-0.00870.21760.2098-0.4379-0.0262-0.0817-0.03510.07990.03480.4315-0.01370.04580.24770.0180.05945.035852.5363-35.2365
117.47451.9152-3.39164.3015-1.51382.1866-0.02670.50660.4594-0.11330.01830.3967-0.236-0.15510.00840.570.0392-0.40850.4470.04290.6071-46.279861.5681-44.9135
120.6685-1.080.12852.1029-0.52060.90590.11480.29640.1708-0.4735-0.3471-0.15190.3240.13650.23240.4359-0.0604-0.02980.28470.18450.2445-0.25655.354-41.1571
131.7399-0.64860.25555.7613-0.83552.3624-0.14860.0235-0.4182-0.0938-0.0341-0.49080.09340.00030.18270.11480.02040.16260.28460.01760.299126.406825.5175-15.6982
1411.16864.6217-1.02316.30353.76446.02770.507-1.0537-0.7670.7055-0.836-1.05040.12920.23070.32910.4376-0.0252-0.21230.34610.42010.652619.14067.37644.3429
154.1781.0221-1.12290.3132-0.29150.3065-0.02580.010.3312-0.20570.0694-0.04820.0524-0.013-0.04351.2477-0.011-0.14311.00330.02140.905231.4669-20.1371-34.9909
161.63771.4412-0.10384.98158.712922.64990.19430.0013-0.3565-0.3378-0.6506-0.4324-0.7352-0.2780.45631.1250.05880.02011.41310.18691.068522.7167-15.5933-37.5698
170.4308-1.57760.59285.7862-2.16010.8425-0.17560.04950.1360.7305-0.1183-0.4603-0.20010.21930.29391.27350.2651-0.06211.48440.02381.02528.4267-5.6683-38.9888
183.11885.211-1.5918.7095-2.66310.82630.2947-0.223-0.20670.5724-0.3559-0.3564-0.29390.12030.06121.66240.2273-0.13031.3002-0.13240.782831.8592-14.4216-43.5517
195.1641-2.72645.16111.8353-2.98655.33140.37091.22630.2028-0.7422-0.6375-0.26320.75861.20180.26650.93390.0903-0.0180.6217-0.10550.3953-37.736640.8508-42.5196
202.91291.55710.97481.9584-1.3894.4983-0.2981-0.20161.44410.7854-0.03890.5953-1.6174-1.20780.3370.95630.2842-0.07150.73340.03991.1632-48.431156.4959-22.1969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 115
2X-RAY DIFFRACTION2A116 - 266
3X-RAY DIFFRACTION3A267 - 443
4X-RAY DIFFRACTION4A444 - 512
5X-RAY DIFFRACTION5A513 - 567
6X-RAY DIFFRACTION6A568 - 768
7X-RAY DIFFRACTION7A769 - 800
8X-RAY DIFFRACTION8B14 - 115
9X-RAY DIFFRACTION9B116 - 266
10X-RAY DIFFRACTION10B267 - 443
11X-RAY DIFFRACTION11B444 - 512
12X-RAY DIFFRACTION12B513 - 567
13X-RAY DIFFRACTION13B568 - 768
14X-RAY DIFFRACTION14B769 - 800
15X-RAY DIFFRACTION15C820 - 838
16X-RAY DIFFRACTION16C839 - 853
17X-RAY DIFFRACTION17D820 - 838
18X-RAY DIFFRACTION18D839 - 853
19X-RAY DIFFRACTION19E1 - 8
20X-RAY DIFFRACTION19F14 - 21
21X-RAY DIFFRACTION20E9 - 20
22X-RAY DIFFRACTION20F2 - 13

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