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- PDB-1w7a: ATP bound MutS -

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Basic information

Entry
Database: PDB / ID: 1w7a
TitleATP bound MutS
Components
  • 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP *CP*AP*CP*CP*AP*GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP*TP* AP*T)-3'
  • 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP *GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP* CP*T)-3'
  • DNA MISMATCH REPAIR PROTEIN MUTS
KeywordsDNA BINDING / ABC ATPASE / ALTERNATING ATPASE / ASYMMETRY / ATP-BINDING / DNA REPAIR / DNA-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
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLamers, M.H. / Georgijevic, D. / Lebbink, J. / Winterwerp, H.H.K. / Agianian, B. / de Wind, N. / Sixma, T.K.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: ATP Increases the Affinity between Muts ATPase Domains: Implications for ATP Hydrolysis and Conformational Changes
Authors: Lamers, M.H. / Georgijevic, D. / Lebbink, J. / Winterwerp, H.H.K. / Agianian, B. / De Wind, N. / Sixma, T.K.
History
DepositionAug 31, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_database_status.status_code_sf / _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.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.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_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
E: 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP *CP*AP*CP*CP*AP*GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP*TP* AP*T)-3'
F: 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP *GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP* CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,7127
Polymers197,6744
Non-polymers1,0393
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)90.636, 93.040, 262.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA MISMATCH REPAIR PROTEIN MUTS /


Mass: 89604.359 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-800
Source method: isolated from a genetically manipulated source
Details: DNA OLIGOMER CONTAINING GT MISMATCH ADENOSINE TRIPHOSPHATE (ATP)
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET3D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23909

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DNA chain , 2 types, 2 molecules EF

#2: 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*GP*CP*GP*TP*CP*CP*TP* AP*T)-3'


Mass: 9184.905 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP *GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP* CP*T)-3'


Mass: 9279.964 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 269 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHIS PROTEIN IS INVOLVED IN THE REPAIR OF MISMATCHES IN DNA. IT CARRIES OUT THE MISMATCH RECOGNITION.

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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: 2.06 Å3/Da / Density % sol: 0.49 %
Crystal growpH: 7.5
Details: 12-14% PEG6000, 150-300MM NACL, 10 MM MGCL2, 25 MM HEPES PH 7.5, 100 UM ADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 10, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 99607 / % possible obs: 99.6 % / Observed criterion σ(I): 1.3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E3M

1e3m


Resolution: 2.27→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.36 / SU ML: 0.277 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2002 2 %RANDOM
Rwork0.216 ---
obs0.217 99607 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2--1.77 Å20 Å2
3----2.81 Å2
Refinement stepCycle: LAST / Resolution: 2.27→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12242 714 63 266 13285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02113333
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212030
X-RAY DIFFRACTIONr_angle_refined_deg1.2942.04618199
X-RAY DIFFRACTIONr_angle_other_deg0.834327913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.57831549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.073152311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1190.22034
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214259
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022527
X-RAY DIFFRACTIONr_nbd_refined0.2220.152888
X-RAY DIFFRACTIONr_nbd_other0.20.1511914
X-RAY DIFFRACTIONr_nbtor_refined0.0380.522
X-RAY DIFFRACTIONr_nbtor_other0.0950.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.5661
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.1521
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.1570
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6171.57739
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.185212425
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8435594
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0364.55774
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
LS refinement shellResolution: 2.27→2.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 122
Rwork0.306 5807
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)
12.1725-0.2297-0.26981.5812-0.15091.93060.07410.0981-0.0690.0110.0473-0.09320.0802-0.0605-0.12140.2032-0.0134-0.02420.2025-0.02160.225239.57910.1133.828
21.9730.3108-0.34051.5438-0.16260.7960.0864-0.025-0.0034-0.12520.04060.00110.0018-0.051-0.12710.1742-0.0355-0.01990.17210.00390.250413.7098.95218.755
30.9864-0.27970.85880.6356-0.74031.71570.0011-0.30270.15810.03510.06020.0873-0.0183-0.1199-0.06130.1876-0.04790.02230.289-0.0310.2726-0.03821.15132.782
43.0784-1.06251.509-3.0822-1.59142.1569-0.2331-0.49730.12110.07010.22560.004-0.3162-0.33380.00740.19490.00660.04540.3612-0.0770.2654-7.76828.25332.148
52.2350.71650.25132.5539-1.46488.4445-0.0815-0.0072-0.00620.03480.24660.0167-0.1768-0.2854-0.16510.33140.0848-0.04380.20190.03370.143642.56716.80777.197
63.9283-0.92743.29571.5182-1.56393.9157-0.1131-0.8652-0.24170.31220.1680.0467-0.0812-0.4798-0.0550.2224-0.02230.04660.52080.0610.14078.8848.80454.082
72.4398-0.05372.5850.24190.28132.22470.20090.0366-0.2090.161-0.00210.01140.3495-0.0198-0.19890.2709-0.1397-0.00230.47740.09990.20218.9294.55454.866
80.76030.1732-0.43750.7621-0.61132.36710.0484-0.07660.0188-0.0062-0.07890.086-0.1440.05850.03050.1869-0.005-0.07680.0977-0.00680.3658-5.33734.2645.252
92.9949-1.7812-0.13480.8826-0.33554.39630.18-0.27180.83070.7755-0.13950.012-0.5748-0.3666-0.04060.30370.048-0.06620.0537-0.03270.6028-8.80951.6396.127
106.1341-0.03591.08942.9171.29562.4398-0.1778-0.21560.3385-0.0140.1620.4409-0.1611-0.02050.01580.19350.10790.040.06060.0350.39221.44760.377-4.937
114.70681.78430.34773.55190.33394.60290.4036-0.6987-0.21120.5782-0.40640.20010.6577-0.56470.00280.4708-0.274-0.04380.32170.02670.247428.74544.65143.738
121.08110.2512-0.08571.8159-0.59921.82640.069-0.07040.105-0.0316-0.03750.167-0.2298-0.2291-0.03140.3210.0016-0.03880.1542-0.05710.253533.44465.57926.043
130.46810.01260.91170.2962-0.06891.47310.0857-0.0488-0.00360.0301-0.05540.0060.10220.0617-0.03020.2643-0.0178-0.02670.1398-0.03140.275947.92252.07313.878
140.1051-0.01880.98550.6263-0.47047.96650.03880.0794-0.1652-0.112-0.08110.09250.16810.57970.04230.23510.0637-0.04440.1643-0.06440.250449.72249.0774.054
152.61481.2512-1.10185.3528-2.55193.1104-0.0588-0.02460.0340.2012-0.188-0.29990.02130.40630.24680.2565-0.0269-0.08090.36310.0750.178562.84918.91262.081
160.9263-0.57571.02891.9614-3.33156.16610.1817-0.08530.08530.099-0.299-0.1056-0.13150.68820.11730.2231-0.0732-0.0750.2216-0.03420.293664.66848.62433.953
170.6312-0.41790.68031.9193-1.37122.34890.054-0.27480.06410.4562-0.1435-0.0776-0.4080.04250.08960.2917-0.1611-0.08530.29380.00470.230261.6248.0544.186
183.73-0.34960.45220.4490.06940.46680.05880.02070.1487-0.0191-0.01760.0546-0.01210.0091-0.04120.24640.0198-0.01890.0702-0.01120.283425.19955.549-6.753
192.49490.16470.03263.8711-0.1975-0.8869-0.0850.1632-0.5135-0.19360.2274-0.56410.0085-0.0358-0.14240.28230.0416-0.06860.1346-0.02880.374723.4440.189-16.533
202.32382.0463-1.24065.2598-3.1783.8166-0.16250.23-0.3281-0.27680.15690.070.0622-0.04740.00560.23550.077-0.07050.1548-0.09490.25786.11434.897-16.272
210.83950.40491.18580.98290.63944.877-0.03740.0382-0.14850.26780.081-0.2854-0.17230.3176-0.04360.2645-0.0273-0.03670.2428-0.01980.267649.93814.68851.271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 115
2X-RAY DIFFRACTION2A116 - 265
3X-RAY DIFFRACTION3A266 - 387
4X-RAY DIFFRACTION4A550 - 567
5X-RAY DIFFRACTION5A444 - 503
6X-RAY DIFFRACTION6A388 - 443
7X-RAY DIFFRACTION7A504 - 549
8X-RAY DIFFRACTION8A568 - 741
9X-RAY DIFFRACTION9A742 - 765
10X-RAY DIFFRACTION10A766 - 800
11X-RAY DIFFRACTION11B2 - 115
12X-RAY DIFFRACTION12B116 - 265
13X-RAY DIFFRACTION13B266 - 387
14X-RAY DIFFRACTION14B550 - 567
15X-RAY DIFFRACTION15B444 - 503
16X-RAY DIFFRACTION16B388 - 443
17X-RAY DIFFRACTION17B504 - 549
18X-RAY DIFFRACTION18B568 - 741
19X-RAY DIFFRACTION19B742 - 765
20X-RAY DIFFRACTION20B766 - 800
21X-RAY DIFFRACTION21E1 - 18
22X-RAY DIFFRACTION21F14 - 30

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