[English] 日本語
Yorodumi
- PDB-2nrr: Crystal structure of the C-terminal RNAseH endonuclase domain of UvrC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nrr
TitleCrystal structure of the C-terminal RNAseH endonuclase domain of UvrC
ComponentsUvrABC system protein C
KeywordsHYDROLASE / UvrC / endonuclase / NER
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / DNA damage response / DNA binding / cytoplasm
Similarity search - Function
UvrC, RNAse H endonuclease domain / : / UvrC, RNAse H endonuclease domain / UvrABC system, subunit C / UvrC, RNAse H endonuclease domain superfamily / UvrC RNAse H endonuclease domain / UvrC family, homology region profile. / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG catalytic domain ...UvrC, RNAse H endonuclease domain / : / UvrC, RNAse H endonuclease domain / UvrABC system, subunit C / UvrC, RNAse H endonuclease domain superfamily / UvrC RNAse H endonuclease domain / UvrC family, homology region profile. / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily / UVR domain superfamily / UvrB/uvrC motif / UVR domain / UVR domain profile. / RuvA domain 2-like / Helix-hairpin-helix domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
UvrABC system protein C
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsKarakas, E. / Truglio, J.J. / Kisker, C.
CitationJournal: Embo J. / Year: 2007
Title: Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad.
Authors: Karakas, E. / Truglio, J.J. / Croteau, D. / Rhau, B. / Wang, L. / Van Houten, B. / Kisker, C.
History
DepositionNov 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UvrABC system protein C


Theoretical massNumber of molelcules
Total (without water)18,6421
Polymers18,6421
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.048, 46.516, 84.501
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein UvrABC system protein C / Protein uvrC / Excinuclease ABC subunit C


Mass: 18642.455 Da / Num. of mol.: 1 / Fragment: C-terminal domain (residues 345-502)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: uvrC / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q9WYA3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.4 M sodium chloride, 0.1 M sodium acetate (pH 4.6) and 0.1 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.0, 1.07249, 1.07114
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.072491
31.071141
ReflectionResolution: 1.2→40 Å / Num. all: 47662 / Num. obs: 47662 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.067 / Χ2: 0.986 / Net I/σ(I): 13.1
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.417 / Num. unique all: 4650 / Χ2: 0.928 / % possible all: 99.2

-
Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
12 wavelength11.071112.35-15.8
12 wavelength21.07257.93-21
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Pt38.610.4120.6530.0920.456
2Pt23.7570.7580.4930.0470.07
3Pt32.7780.3980.7350.0770.165
4Pt15.4850.9920.0040.2170.067
5Pt47.90.940.0280.240.119
6Pt21.350.2890.8730.0470.06
7Pt600.360.6530.2420.1
Phasing dmFOM : 0.64 / FOM acentric: 0.65 / FOM centric: 0.61 / Reflection: 10350 / Reflection acentric: 8761 / Reflection centric: 1589
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-19.6440.910.940.86478308170
3.6-5.70.940.950.8914351116319
2.9-3.60.860.880.7517591462297
2.5-2.90.710.730.5717441502242
2.1-2.50.510.530.3830642696368
2-2.10.30.320.2118701677193

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.07phasing
RESOLVE2.07phasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.2→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.408 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2412 5.1 %RANDOM
Rwork0.183 ---
all0.184 45214 --
obs0.184 47626 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.909 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2--1.57 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1125 0 0 195 1320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221146
X-RAY DIFFRACTIONr_bond_other_d0.0010.021083
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9771544
X-RAY DIFFRACTIONr_angle_other_deg0.87132507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7455135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0823.09155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33815207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0891510
X-RAY DIFFRACTIONr_chiral_restr0.110.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02234
X-RAY DIFFRACTIONr_nbd_refined0.230.2253
X-RAY DIFFRACTIONr_nbd_other0.2060.21103
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2561
X-RAY DIFFRACTIONr_nbtor_other0.0880.2701
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0550.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2650.224
X-RAY DIFFRACTIONr_mcbond_it2.5621.5896
X-RAY DIFFRACTIONr_mcbond_other1.9391.5281
X-RAY DIFFRACTIONr_mcangle_it3.00821117
X-RAY DIFFRACTIONr_scbond_it4.3183516
X-RAY DIFFRACTIONr_scangle_it5.6264.5427
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 177 -
Rwork0.234 3283 -
obs-3460 99.65 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.66970.1819-0.41410.3617-0.37470.601-0.0055-0.04340.00040.0025-0.01260.0119-0.00870.0540.0180.0012-0.0046-0.0205-0.0699-0.00850.0213water30.59829.51914.771
20.1970.023-0.18830.1753-0.15830.34250.0048-0.0188-0.00340.0059-0.0047-0.0015-0.01340.0056-0-0.00630.0009-0.0028-0.0005-0.0028-0.0091protein29.66430.04114.676
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11B1 - 195
22A344 - 4941 - 151

+
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