[English] 日本語
Yorodumi
- PDB-7m4i: DNA Polymerase Lambda, dCTP:At Mn2+ Product State Ternary Complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7m4i
TitleDNA Polymerase Lambda, dCTP:At Mn2+ Product State Ternary Complex, 420 min
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*CP*C)-3')
  • DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA polymerase lambda
KeywordsREPLICATION / Time-Lapse Crystallography / Double Strand Break Repair / DNA Synthesis Fidelity
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-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-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 ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-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 family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / 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
: / PYROPHOSPHATE / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsJamsen, J.A. / Wilson, S.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050158 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050161 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1K99ES029572-01 United States
CitationJournal: Nat Commun / Year: 2022
Title: Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints.
Authors: Jamsen, J.A. / Shock, D.D. / Wilson, S.H.
History
DepositionMar 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: DNA polymerase lambda
T: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
P: DNA (5'-D(*CP*AP*GP*TP*AP*CP*C)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,95014
Polymers43,3524
Non-polymers59810
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-77 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.750, 62.317, 142.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 36703.977 Da / Num. of mol.: 1 / Mutation: C543A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

-
DNA chain , 3 types, 3 molecules TPD

#2: DNA chain DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')


Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*AP*GP*TP*AP*CP*C)-3')


Mass: 2082.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*GP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 5 types, 92 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.79 % / Mosaicity: 0.426 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33609 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.034 / Rrim(I) all: 0.078 / Χ2: 1.144 / Net I/σ(I): 11.2 / Num. measured all: 161791
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.80.82315470.7490.4030.9211.09493.8
2.03-2.074.70.6816200.8170.3340.7621.17596.7
2.07-2.114.90.58616260.830.2870.6561.21598.3
2.11-2.154.80.50316580.8510.2520.5661.27199.5
2.15-2.24.90.42316760.8950.210.4741.26199.9
2.2-2.254.90.35116820.9230.1750.3941.309100
2.25-2.314.80.30116920.9430.150.3381.321100
2.31-2.374.90.24916410.9550.1230.2791.247100
2.37-2.444.90.19716910.9710.0970.221.204100
2.44-2.524.90.1716760.9780.0830.191.22399.9
2.52-2.614.90.1416830.9850.0680.1561.107100
2.61-2.714.90.11716750.9910.0570.131.092100
2.71-2.844.90.09916940.9930.0480.111.123100
2.84-2.994.90.08316900.9940.040.0931.062100
2.99-3.174.80.06917040.9960.0320.0771.047100
3.17-3.424.80.06316980.9950.0290.071.02299.9
3.42-3.764.80.0617120.9950.0280.0661.03499.7
3.76-4.314.80.05817260.9950.0270.0641.01699.5
4.31-5.434.80.05917340.9950.0280.0661.07399
5.43-504.40.05617840.9940.0280.0630.9995

-
Processing

Software
NameVersionClassification
PHENIXv1.15.2-3472refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UPQ

3upq


Resolution: 2.005→37.723 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 1635 4.87 %
Rwork0.2218 31911 -
obs0.223 33546 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.04 Å2 / Biso mean: 59.4261 Å2 / Biso min: 31.31 Å2
Refinement stepCycle: final / Resolution: 2.005→37.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 445 26 82 2836
Biso mean--52.67 56.27 -
Num. residues----340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.005-2.06360.34911100.3239237189
2.0636-2.13020.34311430.3104259198
2.1302-2.20640.28521220.29732637100
2.2064-2.29470.31521430.27392658100
2.2947-2.39910.31141430.25752676100
2.3991-2.52560.2821350.25052671100
2.5256-2.68380.32281370.24252663100
2.6838-2.89090.31161340.23932697100
2.8909-3.18170.27891480.24492694100
3.1817-3.64180.22821330.20482728100
3.6418-4.5870.20871480.18132723100
4.587-37.7230.21751390.2172280297
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)
11.42580.045-0.61131.68160.23971.05420.0601-0.17890.07130.24460.0433-0.0567-0.00460.072800.40690.0228-0.0430.4644-0.0560.4479-13.6885-10.465515.3681
20.1221-0.086-0.04960.09360.07510.0801-0.119-0.5636-0.1643-0.3717-0.00450.40070.03260.037400.6829-0.04130.00150.6720.12670.4642-27.0566-22.691726.5008
30.21880.07790.28430.8068-1.0392.04210.384-0.7123-0.0780.90150.98050.6564-1.1509-0.52690.11720.61790.12820.080.6996-0.02180.5247-27.6958-7.978812.0425
40.1279-0.0849-0.06230.21320.01510.09980.1481-0.46540.00690.3141-0.0358-0.3233-0.4645-0.368100.44330.0072-0.01240.5139-0.06420.389-23.9967-14.00319.89
50.22980.040.07630.51330.68260.91020.6529-0.1434-0.23350.59890.3665-0.34770.04950.07180.04740.9186-0.01010.12090.81680.08330.5696-19.5066-28.180530.0471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 252 through 575)A252 - 575
2X-RAY DIFFRACTION2(chain 'T' and resid 1 through 5)T1 - 5
3X-RAY DIFFRACTION3(chain 'T' and resid 6 through 11)T6 - 11
4X-RAY DIFFRACTION4(chain 'P' and resid 1 through 7)P1 - 7
5X-RAY DIFFRACTION5(chain 'D' and resid 1 through 4)D1 - 4

+
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