[English] 日本語
Yorodumi
- PDB-6mfq: Crystal structure of a PMS2 variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mfq
TitleCrystal structure of a PMS2 variant
ComponentsMismatch repair endonuclease PMS2
KeywordsHYDROLASE / Mismatch Repair / Variant of Uncertain Significance / ATPase Domain / DNA Repair Enzyme
Function / homology
Function and homology information


single base insertion or deletion binding / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / MutLalpha complex / somatic recombination of immunoglobulin gene segments / positive regulation of isotype switching to IgA isotypes / positive regulation of isotype switching to IgG isotypes / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / ATP-dependent DNA damage sensor activity ...single base insertion or deletion binding / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / MutLalpha complex / somatic recombination of immunoglobulin gene segments / positive regulation of isotype switching to IgA isotypes / positive regulation of isotype switching to IgG isotypes / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / ATP-dependent DNA damage sensor activity / somatic hypermutation of immunoglobulin genes / mismatch repair / TP53 Regulates Transcription of DNA Repair Genes / endonuclease activity / Hydrolases; Acting on ester bonds / response to xenobiotic stimulus / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / 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 ...MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / 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 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mismatch repair endonuclease PMS2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsD'Arcy, B.M. / Prakash, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R00ES024417-04 United States
CitationJournal: Hum. Mutat. / Year: 2019
Title: Biochemical and structural characterization of two variants of uncertain significance in the PMS2 gene.
Authors: D'Arcy, B.M. / Blount, J. / Prakash, A.
History
DepositionSep 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mismatch repair endonuclease PMS2
B: Mismatch repair endonuclease PMS2


Theoretical massNumber of molelcules
Total (without water)81,9982
Polymers81,9982
Non-polymers00
Water59433
1
A: Mismatch repair endonuclease PMS2


Theoretical massNumber of molelcules
Total (without water)40,9991
Polymers40,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mismatch repair endonuclease PMS2


Theoretical massNumber of molelcules
Total (without water)40,9991
Polymers40,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.989, 74.962, 134.399
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 33 through 79 or (resid 80...
21(chain B and (resid 33 through 44 or (resid 45...

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
11LEULEUASNASN(chain A and (resid 33 through 79 or (resid 80...AA33 - 7937 - 83
12PHEPHEGLUGLU(chain A and (resid 33 through 79 or (resid 80...AA80 - 8184 - 85
13LEULEUSERSER(chain A and (resid 33 through 79 or (resid 80...AA33 - 36537 - 369
14LEULEUSERSER(chain A and (resid 33 through 79 or (resid 80...AA33 - 36537 - 369
15LEULEUSERSER(chain A and (resid 33 through 79 or (resid 80...AA33 - 36537 - 369
16LEULEUSERSER(chain A and (resid 33 through 79 or (resid 80...AA33 - 36537 - 369
21LEULEUGLUGLU(chain B and (resid 33 through 44 or (resid 45...BB33 - 4437 - 48
22ASNASNASNASN(chain B and (resid 33 through 44 or (resid 45...BB4549
23LEULEUSERSER(chain B and (resid 33 through 44 or (resid 45...BB33 - 36537 - 369
24LEULEUSERSER(chain B and (resid 33 through 44 or (resid 45...BB33 - 36537 - 369
25LEULEUSERSER(chain B and (resid 33 through 44 or (resid 45...BB33 - 36537 - 369
26LEULEUSERSER(chain B and (resid 33 through 44 or (resid 45...BB33 - 36537 - 369

-
Components

#1: Protein Mismatch repair endonuclease PMS2 / DNA mismatch repair protein PMS2 / PMS1 protein homolog 2


Mass: 40998.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMS2, PMSL2 / Variant: G207E / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3 pLysS)
References: UniProt: P54278, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Crystals were obtained in conditions containing 4% tacsimate pH 5 (v/v) and 25% PEG 3350 (w/v). The concentrated PMS2 G207E protein (7 mg/mL) was combined with 0.1ul of an additive (0.1 M ...Details: Crystals were obtained in conditions containing 4% tacsimate pH 5 (v/v) and 25% PEG 3350 (w/v). The concentrated PMS2 G207E protein (7 mg/mL) was combined with 0.1ul of an additive (0.1 M calcium chloride dehydrate) prior to the addition of crystallization reagent in a 1:1 ratio.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.47
ReflectionResolution: 2.6→38.46 Å / Num. obs: 23960 / % possible obs: 100 % / Redundancy: 14.8 % / Biso Wilson estimate: 45.26 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.049 / Rrim(I) all: 0.189 / Χ2: 1 / Net I/σ(I): 12.8
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 15.1 % / Rmerge(I) obs: 1.567 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2361 / CC1/2: 0.584 / Rpim(I) all: 0.416 / Rrim(I) all: 1.62 / Χ2: 1 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.18 Å38.46 Å
Translation5.18 Å38.46 Å

-
Processing

Software
NameVersionClassification
SAINTV8.37Adata reduction
SADABSdata scaling
PHASER2.7.16phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H7S

1h7s


Resolution: 2.6→38.459 Å / Cross valid method: THROUGHOUT / σ(F): 19.68 / Phase error: 23.91
RfactorNum. reflection% reflection
Rfree0.2316 2013 8.41 %
Rwork0.2214 --
obs0.2314 23938 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.28 Å2 / Biso mean: 50.2596 Å2 / Biso min: 35.87 Å2
Refinement stepCycle: final / Resolution: 2.6→38.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 0 33 4511
Biso mean---47.72 -
Num. residues----605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024554
X-RAY DIFFRACTIONf_angle_d0.4966192
X-RAY DIFFRACTIONf_chiral_restr0.042738
X-RAY DIFFRACTIONf_plane_restr0.003806
X-RAY DIFFRACTIONf_dihedral_angle_d5.3372735
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2664X-RAY DIFFRACTION5.778TORSIONAL
12B2664X-RAY DIFFRACTION5.778TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6007-2.66570.33421390.33891530166991
2.6657-2.73780.34191410.3311524166591
2.7378-2.81830.32071380.34611553169191
2.8183-2.90920.34011410.31071555169692
2.9092-3.01320.25471440.28821543168791
3.0132-3.13380.28411420.27151547168992
3.1338-3.27630.27281410.27061550169192
3.2763-3.44890.26931440.25511530167491
3.4489-3.66490.27351410.23831564170592
3.6649-3.94760.2451450.23891579172491
3.9476-4.34440.19771420.19671539168191
4.3444-4.97190.16841440.17931608175292
4.9719-6.25960.21361490.19521611176091
6.2596-38.46330.23111600.18271681184191

+
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://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