[English] 日本語
Yorodumi
- PDB-2ok2: MutS C-terminal domain fused to Maltose Binding Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ok2
TitleMutS C-terminal domain fused to Maltose Binding Protein
ComponentsMaltose-binding periplasmic protein, DNA mismatch repair protein mutS fusion protein
KeywordsSUGAR BINDING PROTEIN / DNA REPAIR / MISMATCH REPAIR / TETRAMERIZATION
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 / detection of maltose stimulus / maltose transport complex / carbohydrate transport ...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 / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / mismatch repair / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / ADP binding / outer membrane-bounded periplasmic space / damaged DNA binding / periplasmic space / DNA damage response / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Helix Hairpins - #430 / 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 ...Helix Hairpins - #430 / 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 / Helix Hairpins / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / Helix non-globular / Special / D-Maltodextrin-Binding Protein; domain 2 / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPutnam, C.D. / Mendillo, M.L. / Kolodner, R.D.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Escherichia coli MutS Tetramerization Domain Structure Reveals That Stable Dimers but Not Tetramers Are Essential for DNA Mismatch Repair in Vivo.
Authors: Mendillo, M.L. / Putnam, C.D. / Kolodner, R.D.
History
DepositionJan 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.classification
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose-binding periplasmic protein, DNA mismatch repair protein mutS fusion protein
B: Maltose-binding periplasmic protein, DNA mismatch repair protein mutS fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5675
Polymers88,7862
Non-polymers7813
Water9,206511
1
A: Maltose-binding periplasmic protein, DNA mismatch repair protein mutS fusion protein
B: Maltose-binding periplasmic protein, DNA mismatch repair protein mutS fusion protein
hetero molecules

A: Maltose-binding periplasmic protein, DNA mismatch repair protein mutS fusion protein
B: Maltose-binding periplasmic protein, DNA mismatch repair protein mutS fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,13410
Polymers177,5734
Non-polymers1,5616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)174.289, 88.361, 61.353
Angle α, β, γ (deg.)90.00, 106.80, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the crystallographic two fold axis: -x+1,y,-z.

-
Components

#1: Protein Maltose-binding periplasmic protein, DNA mismatch repair protein mutS fusion protein


Mass: 44393.176 Da / Num. of mol.: 2 / Fragment: MBP/MutS C-terminal fusion
Source method: isolated from a genetically manipulated source
Details: Residues 1-368 are from MBP, residues 369-402 are from MutS (residues 820-853)
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: malE / Plasmid: pRDK1234 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Tn10::mutS / References: UniProt: P0AEX9, UniProt: P23909
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 4K, 100 mM sodium citrate, 100 mM lithium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2006
Details: Crystal type: Si(111) Mirrors: Rh coated flat mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 59119 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 35 Å2 / Rsym value: 0.058 / Net I/σ(I): 47
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 5746 / Rsym value: 0.548 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FQC

1fqc


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.45 / SU ML: 0.181 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC + TLS REFINEMENT / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27725 2991 5.1 %RANDOM
Rwork0.20125 ---
all0.20501 58980 --
obs0.20501 55989 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.559 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å20 Å2-1.94 Å2
2--1.8 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 51 511 6828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226541
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.9758903
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3625816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50825.923287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.964151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7931514
X-RAY DIFFRACTIONr_chiral_restr0.1270.2978
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024972
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.23238
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.24517
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2505
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0231.54193
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44326516
X-RAY DIFFRACTIONr_scbond_it2.61432767
X-RAY DIFFRACTIONr_scangle_it3.6524.52387
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 214 -
Rwork0.293 4056 -
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)
11.40127.5551-12.12840.7359-65.3924104.9731.4410.38470.84854.0287-2.778-2.2948-4.20962.63011.3370.40380.14890.05840.5118-0.08870.42883.0152-8.559-3.9657
23.9044-1.10920.5923.557-0.26793.4280.30130.5285-0.3393-0.2297-0.3139-0.08030.15220.35660.0126-0.07740.11330.02760.0648-0.1504-0.055668.2728-6.45753.423
32.65070.1847-0.30654.32510.42573.120.14860.0499-0.21720.13290.0683-0.1377-0.19130.068-0.2169-0.187-0.02550.0974-0.2185-0.0202-0.158953.539710.038523.0099
41.9959-0.8648-0.19471.96431.16952.62570.12610.2662-0.35870.04780.0384-0.1920.11870.2443-0.1645-0.1626-0.02450.0241-0.1149-0.0777-0.038660.85360.462115.0987
515.9268-0.317516.9053.2561-1.703418.5177-0.1406-1.8877-0.42010.03020.21650.11770.5837-2.8207-0.0760.0691-0.09110.15850.166-0.0013-0.161776.819814.5886-4.5823
634.18566.14144.200146.967210.149841.4991-0.64731.21150.7799-0.89060.94530.03552.4504-1.4808-0.2980.34710.0185-0.07140.3381-0.11770.334496.142639.1385-10.5888
74.08750.18032.09480.6227-0.09723.41130.23340.4766-0.48840.20690.194-0.38640.15110.4839-0.4274-0.04430.124-0.1224-0.0403-0.23050.105680.559346.0387-13.884
83.40390.32720.64762.0044-0.42373.72310.25880.3254-0.34350.10490.2301-0.07310.15830.2451-0.4889-0.11090.1246-0.0346-0.1031-0.1333-0.047257.187139.9117-29.6882
93.71340.492.82830.75690.33842.156-0.06780.9112-0.12710.05540.2603-0.3356-0.160.6621-0.1925-0.10170.07840.02590.1591-0.1763-0.034474.505149.9353-25.4587
102.30420.79420.81071.4414-0.05972.58650.28720.2136-0.22010.23710.0253-0.02720.19370.238-0.31240.00390.147-0.0992-0.0564-0.10890.020461.955140.3557-20.3902
1110.147-4.26075.29623.6788-3.98644.4083-1.3884-1.34691.34210.41910.9581-0.0217-1.2402-1.24340.43040.34550.226-0.19660.1382-0.160.102575.208324.6265-6.2431
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 61 - 6
2X-RAY DIFFRACTION2AA7 - 1107 - 110
3X-RAY DIFFRACTION3AA111 - 205111 - 205
4X-RAY DIFFRACTION4AA206 - 375206 - 375
5X-RAY DIFFRACTION5AA376 - 402376 - 402
6X-RAY DIFFRACTION6BB1 - 61 - 6
7X-RAY DIFFRACTION7BB7 - 1157 - 115
8X-RAY DIFFRACTION8BB116 - 212116 - 212
9X-RAY DIFFRACTION9BB213 - 307213 - 307
10X-RAY DIFFRACTION10BB308 - 367308 - 367
11X-RAY DIFFRACTION11BB368 - 402368 - 402

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more