[English] 日本語
Yorodumi
- PDB-2gws: Crystal Structure of human DNA Polymerase lambda with a G/G misma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gws
TitleCrystal Structure of human DNA Polymerase lambda with a G/G mismatch in the primer terminus
Components
  • 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
  • 5'-D(*GP*TP*GP*CP*GP*G)-3'
  • 5'-D(P*GP*CP*CP*G)-3'
  • DNA polymerase lambda
KeywordsTransferase/DNA / DNA polymerase lambda / family X / mismatch extension / mutagenesis / NHEJ / Transferase-DNA COMPLEX
Function / homology
Function and homology information


DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break ...DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGarcia-Diaz, M. / Picher, A.J. / Bebenek, K. / Pedersen, L.C. / Kunkel, T.A. / Blanco, L.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Promiscuous mismatch extension by human DNA polymerase lambda.
Authors: Picher, A.J. / Garcia-Diaz, M. / Bebenek, K. / Pedersen, L.C. / Kunkel, T.A. / Blanco, L.
History
DepositionMay 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
T: 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
P: 5'-D(*GP*TP*GP*CP*GP*G)-3'
D: 5'-D(P*GP*CP*CP*G)-3'
F: 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
G: 5'-D(*GP*TP*GP*CP*GP*G)-3'
H: 5'-D(P*GP*CP*CP*G)-3'
J: 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
K: 5'-D(*GP*TP*GP*CP*GP*G)-3'
L: 5'-D(P*GP*CP*CP*G)-3'
N: 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
R: 5'-D(*GP*TP*GP*CP*GP*G)-3'
Q: 5'-D(P*GP*CP*CP*G)-3'
A: DNA polymerase lambda
E: DNA polymerase lambda
I: DNA polymerase lambda
M: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,30331
Polymers175,52416
Non-polymers77915
Water14,394799
1
T: 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
P: 5'-D(*GP*TP*GP*CP*GP*G)-3'
D: 5'-D(P*GP*CP*CP*G)-3'
A: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1229
Polymers43,8814
Non-polymers2415
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
G: 5'-D(*GP*TP*GP*CP*GP*G)-3'
H: 5'-D(P*GP*CP*CP*G)-3'
E: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1278
Polymers43,8814
Non-polymers2464
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
J: 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
K: 5'-D(*GP*TP*GP*CP*GP*G)-3'
L: 5'-D(P*GP*CP*CP*G)-3'
I: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0416
Polymers43,8814
Non-polymers1602
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
N: 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
R: 5'-D(*GP*TP*GP*CP*GP*G)-3'
Q: 5'-D(P*GP*CP*CP*G)-3'
M: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0128
Polymers43,8814
Non-polymers1314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)192.374, 98.268, 104.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe asymmetric unit contains four biological units

-
Components

-
DNA chain , 3 types, 12 molecules TFJNPGKRDHLQ

#1: DNA chain
5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'


Mass: 3344.188 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: DNA chain
5'-D(*GP*TP*GP*CP*GP*G)-3'


Mass: 1865.240 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: DNA chain
5'-D(P*GP*CP*CP*G)-3'


Mass: 1191.818 Da / Num. of mol.: 4 / Source method: obtained synthetically

-
Protein , 1 types, 4 molecules AEIM

#4: Protein
DNA polymerase lambda / / Pol Lambda / DNA polymerase kappa / DNA polymerase beta-2 / Pol beta2


Mass: 37479.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

-
Non-polymers , 6 types, 814 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 799 / 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: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 6% MPD, 50 mM Na Cacodylate, 100 mM NaCl, 50 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Na Cacodylate11
3NaClSodium chloride11
4MgCl211
5H2O11
6MPD12
7Na Cacodylate12
8NaClSodium chloride12
9MgCl212

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 76713 / % possible obs: 98.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.131 / Χ2: 1.078 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.493.20.53772331.159194.5
2.49-2.593.30.41974061.133196.5
2.59-2.73.50.3475841.215198.5
2.7-2.853.90.28876531.152199.7
2.85-3.024.20.2377081.078199.8
3.02-3.264.30.17977431.122199.9
3.26-3.584.60.14677411.052199.9
3.58-4.15.20.13477811.055199.9
4.1-5.176.60.12678631.014199.9
5.17-506.60.07980011.004198

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1RZT

1rzt


Resolution: 2.4→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.253 3654 4.7 %
Rwork0.209 --
obs-72337 92.2 %
Solvent computationBsol: 34.197 Å2
Displacement parametersBiso mean: 44.689 Å2
Baniso -1Baniso -2Baniso -3
1--0.157 Å20 Å20 Å2
2---1.952 Å20 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10026 1716 33 799 12574
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2461.5
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_mcangle_it2.0182
X-RAY DIFFRACTIONc_scangle_it2.8122.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4ggmpd2.par

+
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