[English] 日本語
Yorodumi
- PDB-6zgq: AceL NrdHF class 3 split intein GSH linked splice inactive varian... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zgq
TitleAceL NrdHF class 3 split intein GSH linked splice inactive variant - C124A, N146A
ComponentsAceL NrdHF-1-1 Intein
KeywordsSPLICING
Function / homologyEndonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Beta Complex / Mainly Beta / IODIDE ION
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHoffmann, S. / Mootz, H.D. / Kuemmel, D. / Singh, R.
Funding support1items
OrganizationGrant numberCountry
German Research Foundation (DFG)
CitationJournal: Chembiochem / Year: 2021
Title: Biochemical and Structural Characterization of an Unusual and Naturally Split Class 3 Intein.
Authors: Hoffmann, S. / Terhorst, T.M.E. / Singh, R.K. / Kummel, D. / Pietrokovski, S. / Mootz, H.D.
History
DepositionJun 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AceL NrdHF-1-1 Intein
B: AceL NrdHF-1-1 Intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0729
Polymers37,1842
Non-polymers8887
Water3,459192
1
A: AceL NrdHF-1-1 Intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9734
Polymers18,5921
Non-polymers3813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AceL NrdHF-1-1 Intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1005
Polymers18,5921
Non-polymers5084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.504, 45.060, 46.281
Angle α, β, γ (deg.)65.450, 77.510, 69.350
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein AceL NrdHF-1-1 Intein


Mass: 18591.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.71 %
Crystal growTemperature: 305 K / Method: vapor diffusion, hanging drop / Details: PEG3350 25 %, Glycerol 20 %, 0.1 M MIB

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.5498 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 1.9→41.96 Å / Num. obs: 20988 / % possible obs: 93.6 % / Redundancy: 3.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.058 / Rrim(I) all: 0.107 / Net I/σ(I): 7.1 / Num. measured all: 72086
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.943.50.411442212750.8560.2620.49289.1
9.11-41.963.10.0596011930.9940.0390.07116.395.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→41.96 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.883 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 1070 5.1 %RANDOM
Rwork0.2257 ---
obs0.2272 19917 93.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 291.7 Å2 / Biso mean: 15.512 Å2 / Biso min: 4.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å21.64 Å22.02 Å2
2--0.73 Å2-0.16 Å2
3---0.69 Å2
Refinement stepCycle: final / Resolution: 1.9→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 7 192 2639
Biso mean--51.53 46.15 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192575
X-RAY DIFFRACTIONr_bond_other_d0.0010.022414
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9513490
X-RAY DIFFRACTIONr_angle_other_deg0.72635616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4445327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44125.691123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84415478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.135158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022951
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02555
X-RAY DIFFRACTIONr_rigid_bond_restr2.2134989
X-RAY DIFFRACTIONr_sphericity_free531
X-RAY DIFFRACTIONr_sphericity_bonded24.09655101
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 88 -
Rwork0.288 1400 -
all-1488 -
obs--89.32 %

+
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