[English] 日本語
Yorodumi
- PDB-5x9w: Mismatch Repair Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x9w
TitleMismatch Repair Protein
ComponentsDNA mismatch repair protein MutS
KeywordsDNA BINDING PROTEIN / DNA Mismatch Repair / Sensor protein / AMPPnP
Function / homology
Function and homology information


mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / damaged DNA binding / ATP binding
Similarity search - Function
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 ...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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsNair, D.T. / Nirwal, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology India
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Mechanism of formation of a toroid around DNA by the mismatch sensor protein.
Authors: Nirwal, S. / Kulkarni, D.S. / Sharma, A. / Rao, D.N. / Nair, D.T.
History
DepositionMar 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA mismatch repair protein MutS
B: DNA mismatch repair protein MutS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,8204
Polymers179,8072
Non-polymers1,0122
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area67300 Å2
ΔGint-37.5 kcal/mol
Surface area5450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.510, 102.070, 235.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.992137, 0.008171, -0.124887), (0.000637, -0.997523, -0.070332), (-0.125153, -0.069859, 0.989675)44.89689, -52.53273, 1.84056

-
Components

#1: Protein DNA mismatch repair protein MutS


Mass: 89903.602 Da / Num. of mol.: 2 / Fragment: UNP residues 1-814
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria)
Strain: ATCC 700825 / FA 1090 / Gene: mutS, NGO1930 / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: Q5F5J4
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-14% (w/v) PEG 4000, 0.1M MES buffer (pH 6.5), 10-14% (v/v) glycerol, 0.1-0.2 M MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 32442 / % possible obs: 98.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.127 / Net I/av σ(I): 8.5 / Net I/σ(I): 8.5
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.5 / % possible all: 98.9

-
Processing

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

1e3m


Resolution: 3.3→49.93 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.895 / SU B: 59.245 / SU ML: 0.45 / Cross valid method: THROUGHOUT / ESU R Free: 0.575 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27292 1646 5.1 %RANDOM
Rwork0.22126 ---
obs0.2239 30777 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 109.139 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å2-0 Å20 Å2
2--2.83 Å2-0 Å2
3----4.29 Å2
Refinement stepCycle: 1 / Resolution: 3.3→49.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11820 0 62 0 11882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912104
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211750
X-RAY DIFFRACTIONr_angle_refined_deg1.331.96816428
X-RAY DIFFRACTIONr_angle_other_deg0.816326936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44851536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66424.06532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.217152026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9791580
X-RAY DIFFRACTIONr_chiral_restr0.0690.21900
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113762
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022748
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_it6.3016.6746162
X-RAY DIFFRACTIONr_mcbond_other6.36.6746161
X-RAY DIFFRACTIONr_mcangle_it10.14210.0057692
X-RAY DIFFRACTIONr_mcangle_other10.14210.0057693
X-RAY DIFFRACTIONr_scbond_it5.5827.0565941
X-RAY DIFFRACTIONr_scbond_other5.5817.0565942
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.16410.4148737
X-RAY DIFFRACTIONr_long_range_B_refined17.10762.91650408
X-RAY DIFFRACTIONr_long_range_B_other17.10762.91650409
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 6992 / Type: tight thermal / Rms dev position: 18.98 Å / Weight position: 0.5
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 111 -
Rwork0.279 2272 -
obs--98.47 %
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)
12.7189-0.3139-2.81570.27080.15053.77560.04170.2374-0.1497-0.06880.0407-0.04730.0734-0.1313-0.08240.3213-0.03220.01940.50020.00870.33573.8185-3.5294-12.0673
21.6743-0.41390.81552.43640.03053.07050.0525-0.0224-0.0162-0.152-0.0656-0.1515-0.1686-0.47860.01320.30810.00270.02330.50740.03170.279414.992911.2335-34.7043
30.43420.53740.48853.05671.20280.75680.0779-0.06750.0093-0.7845-0.0691-0.2593-0.10720.0721-0.00870.64020.07840.19890.39090.07130.259636.0506-10.6377-53.2346
41.8792-0.4071-2.81730.62670.71614.32140.0373-0.34430.0869-0.04050.0973-0.0958-0.20530.4637-0.13460.3268-0.1011-0.02070.5675-0.01370.339140.31067.9536-23.3629
50.83950.973-1.91131.9818-2.22276.96240.1574-0.00220.15350.34520.10940.0947-0.3711-0.0705-0.26680.38950.0318-0.02870.5852-0.03870.145221.22925.886916.8195
62.4772-0.51682.87620.4913-0.74274.8063-0.08820.2319-0.18810.08720.19130.1318-0.77360.2147-0.10310.4587-0.05350.19740.2794-0.01740.430742.5325-48.1435-12.3257
71.613-0.121-0.3673.4969-1.21213.9473-0.0714-0.0618-0.0892-0.22010.14530.17160.08150.6849-0.07390.12660.01150.07390.29350.04680.488534.1716-61.7181-37.0075
80.45960.246-0.19484.3002-1.76590.96240.0653-0.0996-0.2969-1.05390.13230.81670.0855-0.114-0.19760.77010.0857-0.33860.1080.0230.519715.8182-37.8851-56.0365
91.1529-0.03280.94952.3716-0.36224.0688-0.2363-0.3652-0.32970.08970.17381.15040.089-0.33740.06250.0910.07310.21550.18680.2050.99697.6858-58.9772-29.0126
101.525-0.20352.30572.22592.59457.64840.1264-0.8598-0.44930.24190.3140.33530.4304-0.7065-0.44040.41850.03770.36710.93620.41060.550721.6522-58.609213.4576
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 120
2X-RAY DIFFRACTION2A123 - 261
3X-RAY DIFFRACTION3A263 - 310
4X-RAY DIFFRACTION3A560 - 785
5X-RAY DIFFRACTION3A901
6X-RAY DIFFRACTION4A313 - 393
7X-RAY DIFFRACTION4A532 - 558
8X-RAY DIFFRACTION5A395 - 531
9X-RAY DIFFRACTION6B1 - 120
10X-RAY DIFFRACTION7B123 - 261
11X-RAY DIFFRACTION8B263 - 310
12X-RAY DIFFRACTION8B560 - 785
13X-RAY DIFFRACTION8B901
14X-RAY DIFFRACTION9B313 - 393
15X-RAY DIFFRACTION9B532 - 558
16X-RAY DIFFRACTION10B395 - 531

+
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