[English] 日本語
Yorodumi
- PDB-3v4r: Crystal structure of a UvrB dimer-DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v4r
TitleCrystal structure of a UvrB dimer-DNA complex
Components
  • DNA: 5 -TACTGTTT-3
  • UvrABC system protein B
KeywordsHYDROLASE/DNA / Helicase motifs and a beta-hairpin / DNA helicase / UvrA / ATP hydrolysis / HYDROLASE-DNA complex
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Helix Hairpins - #240 / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / UVR domain superfamily / UvrB/uvrC motif / UvrB, interaction domain / UvrB interaction domain ...Helix Hairpins - #240 / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / UVR domain superfamily / UvrB/uvrC motif / UvrB, interaction domain / UvrB interaction domain / UVR domain / UVR domain profile. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helix Hairpins / Helix non-globular / Helicase conserved C-terminal domain / Special / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / UvrABC system protein B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsWebster, M.P.J. / Jukes, R. / Barrett, T.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal structure of the UvrB dimer: insights into the nature and functioning of the UvrAB damage engagement and UvrB-DNA complexes.
Authors: Webster, M.P. / Jukes, R. / Zamfir, V.S. / Kay, C.W. / Bagneris, C. / Barrett, T.
History
DepositionDec 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
A: UvrABC system protein B
B: UvrABC system protein B
C: DNA: 5 -TACTGTTT-3
D: DNA: 5 -TACTGTTT-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,2086
Polymers159,3534
Non-polymers8542
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-49 kcal/mol
Surface area50140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.940, 100.310, 163.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit is comprised of a UvrB dimer, two DNA 7mers and 2 molecules of ADP

-
Components

#1: Protein UvrABC system protein B / Protein UvrB / Excinuclease ABC subunit B / Protein DinA


Mass: 77269.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU35170, dinA, uvr, uvrB / Plasmid: pET 8c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P37954, EC: 3.1.21.5
#2: DNA chain DNA: 5 -TACTGTTT-3


Mass: 2407.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesised DNA
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 289 K / Method: microbatch / pH: 6.5
Details: Crystals were grown from 0.1M MES ph 6.5, 12% PEG 20,0000, Microbatch, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 2006 / Details: Mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.25→19.91 Å / Num. all: 25439 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 89.37 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 9.3
Reflection shellResolution: 3.25→3.33 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 2.72 / Num. unique all: 13804 / % possible all: 100

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Protein co-ordinates from 2D7D

2d7d


Resolution: 3.25→19.91 Å / Cor.coef. Fo:Fc: 0.9306 / Cor.coef. Fo:Fc free: 0.9044 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 1297 5.11 %RANDOM
Rwork0.1797 ---
all0.1817 25439 --
obs0.1817 25392 99.98 %-
Displacement parametersBiso mean: 68.8 Å2
Baniso -1Baniso -2Baniso -3
1--10.2322 Å20 Å20 Å2
2--12.1259 Å20 Å2
3----1.8937 Å2
Refine analyzeLuzzati coordinate error obs: 0.522 Å
Refinement stepCycle: LAST / Resolution: 3.25→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8526 254 35 0 8815
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018998HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2212331HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d20.953000SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes0.0076183HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0.01311358HARMONIC5
X-RAY DIFFRACTIONt_it0.018998HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion20.97
X-RAY DIFFRACTIONt_chiral_improper_torsion20.951292SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact20.959787SEMIHARMONIC4
LS refinement shellResolution: 3.25→3.38 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2877 153 5.41 %
Rwork0.2237 2677 -
all0.2271 2830 -
obs--99.98 %
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)
11.25860.198-0.35091.0715-0.15621.0667-0.00080.0412-0.05820.1742-0.0057-0.0189-0.07040.11420.0065-0.11330.0529-0.0344-0.1178-0.0424-0.13665.6313-0.5597-49.2851
21.0841-0.6608-0.00531.80010.29620.743-0.0829-0.0311-0.21180.0870.04910.24270.1406-0.0730.0338-0.1885-0.0764-0.0709-0.03870.02-0.1301-20.88233.6926-70.902
32.62610.76551.9961.1737-1.05010.5323-0.00210.08440.0394-0.04870.0052-0.01590.01220.0388-0.0031-0.07910.0645-0.10750.0628-0.04390.0993-15.3139.5494-73.3775
40.0110.50171.54452.26841.46651.29260.00270.0651-0.08450.05080.0282-0.02450.02720.0718-0.0310.1154-0.1008-0.0960.00380.0065-0.08034.0902-8.304-52.5323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 701
2X-RAY DIFFRACTION2{ B|* }B3 - 701
3X-RAY DIFFRACTION3{ C|* }C2 - 8
4X-RAY DIFFRACTION4{ D|* }D2 - 8

+
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