[English] 日本語
Yorodumi
- PDB-7rcb: Crystal Structure of a PMS2 VUS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rcb
TitleCrystal Structure of a PMS2 VUS
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 / mismatch repair / somatic hypermutation of immunoglobulin genes / 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Mismatch repair endonuclease PMS2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsD'Arcy, B.M. / Prakash, A.
CitationJournal: Mol Genet Genomic Med / Year: 2022
Title: PMS2 variant results in loss of ATPase activity without compromising mismatch repair.
Authors: D'Arcy, B.M. / Arrington, J. / Weisman, J. / McClellan, S.B. / Yang, Z. / Deivanayagam, C. / Blount, J. / Prakash, A.
History
DepositionJul 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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)80,9722
Polymers80,9722
Non-polymers00
Water7,224401
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.219, 75.262, 134.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 33 through 44 or resid 46...
d_2ens_1(chain "B" and (resid 33 through 44 or resid 46...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUGLUA2 - 13
d_12ens_1SERTHRA15 - 53
d_13ens_1ALAASPA58 - 281
d_14ens_1GLUASPA286 - 303
d_21ens_1LEUGLUB1 - 12
d_22ens_1SERTHRB14 - 52
d_23ens_1ALAASPB54 - 295

NCS oper: (Code: givenMatrix: (-0.00682959365487, 0.99986708062, -0.0148046527549), (0.999447839435, 0.00634380433234, -0.0326155238337), (-0.0325172707782, -0.0150192289841, -0.999358319054)Vector: - ...NCS oper: (Code: given
Matrix: (-0.00682959365487, 0.99986708062, -0.0148046527549), (0.999447839435, 0.00634380433234, -0.0326155238337), (-0.0325172707782, -0.0150192289841, -0.999358319054)
Vector: -16.1617809975, 17.6195503895, -100.853549334)

-
Components

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


Mass: 40486.207 Da / Num. of mol.: 2 / Mutation: N335S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMS2, PMSL2 / Plasmid: pET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 (DE3 pLysS)
References: UniProt: P54278, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 1:1 7.5 mg/mL protein with 8% v/v Tacsimate, pH 5.8, 25% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→34.34 Å / Num. obs: 51950 / % possible obs: 98.83 % / Redundancy: 7.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07765 / Rpim(I) all: 0.02862 / Rrim(I) all: 0.083 / Χ2: 1 / Net I/σ(I): 19.71
Reflection shellResolution: 2→2.071 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.8954 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5160 / CC1/2: 0.739 / CC star: 0.922 / Rpim(I) all: 0.3435 / Rrim(I) all: 0.9616 / Χ2: 1 / % possible all: 99.46

-
Processing

Software
NameVersionClassification
SAINTdata reduction
SADABSdata scaling
PHASERphasing
PHENIXV1.19refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1H7S

1h7s


Resolution: 2→34.34 Å / Cross valid method: FREE R-VALUE / σ(F): 15.57 / Phase error: 24.2702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1979 5321 10.24 %
Rwork0.1617 46629 -
obs0.167 51950 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.37 Å2
Refinement stepCycle: LAST / Resolution: 2→34.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 0 401 4888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034571
X-RAY DIFFRACTIONf_angle_d0.57796202
X-RAY DIFFRACTIONf_chiral_restr0.0438736
X-RAY DIFFRACTIONf_plane_restr0.0047801
X-RAY DIFFRACTIONf_dihedral_angle_d12.52051635
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.825705043177 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.32862450.26942232X-RAY DIFFRACTION85.95
2.03-2.070.29412570.25942305X-RAY DIFFRACTION89.65
2.07-2.110.28812880.23932282X-RAY DIFFRACTION88.42
2.11-2.150.23232760.23072370X-RAY DIFFRACTION89.5
2.15-2.20.24472690.21472295X-RAY DIFFRACTION89.33
2.2-2.250.21842870.20572303X-RAY DIFFRACTION88.65
2.25-2.310.21382330.20212362X-RAY DIFFRACTION90.85
2.31-2.370.23212370.19932392X-RAY DIFFRACTION90.71
2.37-2.440.23242820.18662292X-RAY DIFFRACTION88.8
2.44-2.520.23312520.1842356X-RAY DIFFRACTION89.96
2.52-2.610.19392620.17162353X-RAY DIFFRACTION89.64
2.61-2.710.24272750.16982321X-RAY DIFFRACTION88.96
2.71-2.830.20542640.17372334X-RAY DIFFRACTION89.36
2.83-2.980.18952670.1632355X-RAY DIFFRACTION89.2
2.98-3.170.19712320.15662378X-RAY DIFFRACTION89.87
3.17-3.410.17222250.14512382X-RAY DIFFRACTION89.95
3.42-3.760.19352820.13792327X-RAY DIFFRACTION87.51
3.76-4.30.15762940.12662323X-RAY DIFFRACTION87.07
4.3-5.420.15112880.12012325X-RAY DIFFRACTION85.76
5.42-34.340.2022520.16082396X-RAY DIFFRACTION84.57
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)
11.56395605117-0.5709828386660.02966690572461.92052651333-0.4067108285621.07662227917-0.0460890843316-0.0941692511304-0.09676456457790.0892561684051-0.0164831021914-0.08223978190290.01373844509570.1156112196620.06036445314350.202707708917-0.00670284525865-0.008407227500770.1291281216513.66301397892E-50.1246481019584.763686938375.44969592043-38.3090555527
21.57708494367-0.765804967035-0.9382455866013.002743667641.826176273822.18133603619-0.0148112414719-0.143418044249-0.02825693443360.441673215459-0.1443032642230.3736718009270.30598921822-0.2187595821970.1077708527420.248653493438-0.03789653411140.04071734439910.1828727571570.0007141523008840.218860121273-18.550815236119.8223835085-28.4890067983
34.950875821620.08757697181980.278885227121.7604101342-0.03548662569241.26927309039-0.08426955620860.04866115430790.313067073951-0.003819879073380.124414696817-0.146900003326-0.02842460167060.105806209728-0.001611343207210.237245669386-0.00854288240844-0.01640431898820.231817722621-0.01069564781850.167894252742-6.5857564624420.1452996278-61.576038217
44.310627199740.6320168840232.248709675161.333651745371.262542523131.87424347552-0.1087308965370.5678146066390.634257101225-0.2553814722120.168898081522-0.33389867471-0.536554923570.3967062358940.05507984694390.346923511788-0.0877756501458-0.01702527964260.3826755568070.06767770519180.365175584562-8.3110144253933.2618266099-67.3325853236
53.04947977927-1.071769304360.1384257285251.50364380685-0.3177527466061.09920553947-0.131893896063-0.01737977590520.2691467178940.01620426048860.134871066318-0.0112378773622-0.1688978472270.03786126196990.002885257903760.220089632604-0.00710532707418-0.01601496262160.203819822529-0.002068171474160.110617042832-12.183823940123.5704859933-62.0924850376
62.47734816007-0.605241516996-1.199516463471.546341526320.669341227211.81638963915-0.244032825380.280314200722-0.335856994633-0.2061505150490.0934865427932-0.09460342478240.1936202950340.0226113618910.154064147460.261242046946-0.05268123516360.04737896840170.216930107739-0.03298943822140.1812334733984.588541506962.30639569681-67.1029890082
71.83840327204-0.28095352462-0.9509366924651.649155071511.214943764481.47979229975-0.3449256165440.617673553088-0.52712990789-0.3634299453130.05081349645260.1738313397920.50034030115-0.556557311870.3587421076430.458859588211-0.1586798948690.04779233601350.478067851714-0.1343860517690.327850069088-0.68190588309-4.37763131258-73.8909546147
83.72315043276-0.317742283824-1.259536271990.9791727555311.592890046392.78171945802-0.3136367164360.722825016122-0.388010112622-0.579212496993-0.0493366126973-0.1897699294230.206815973192-0.3975514759740.1097020080130.419518938469-0.07526049144570.08778634468810.397369017819-0.08954341888970.2489651912249.814016084970.404078434862-79.1067529146
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 32 through 194 )AA32 - 1941 - 142
22chain 'A' and (resid 195 through 365 )AA195 - 365143 - 304
33chain 'B' and (resid 33 through 76 )BB33 - 761 - 44
44chain 'B' and (resid 77 through 117 )BB77 - 11745 - 61
55chain 'B' and (resid 118 through 194 )BB118 - 19462 - 138
66chain 'B' and (resid 195 through 274 )BB195 - 274139 - 218
77chain 'B' and (resid 275 through 320 )BB275 - 320219 - 264
88chain 'B' and (resid 321 through 364 )BB321 - 364265 - 295

+
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