[English] 日本語
Yorodumi
- PDB-5uxg: Protein 84 with aldehyde deformylating oxygenase activity from Su... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uxg
TitleProtein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (monoclinic)
Componentsaldehyde deformylating oxygenase
KeywordsLYASE / decarbonylase / iron / ferritin
Function / homologyRibonucleotide reductase-like / Ferritin-like superfamily / oxidoreductase activity / metal ion binding / PHOSPHATE ION / Uncharacterized protein
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsWilson, D.K. / Mak, W.S. / Siegel, J.B.
CitationJournal: To Be Published
Title: Protein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (monoclinic)
Authors: Wilson, D.K. / Mak, W.S. / Siegel, J.B.
History
DepositionFeb 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: aldehyde deformylating oxygenase
B: aldehyde deformylating oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1215
Polymers51,8362
Non-polymers2853
Water3,819212
1
A: aldehyde deformylating oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1083
Polymers25,9181
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: aldehyde deformylating oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0132
Polymers25,9181
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.536, 64.849, 71.299
Angle α, β, γ (deg.)90.00, 116.86, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein aldehyde deformylating oxygenase


Mass: 25917.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea)
Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: ST1620, STK_16200 / Production host: Escherichia coli (E. coli) / References: UniProt: Q970H5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Potassium phosphate, PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.72→63.61 Å / Num. obs: 55207 / % possible obs: 96.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.2
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.7 / % possible all: 57

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: theoretical

Resolution: 1.72→63.61 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.494 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22341 1647 3.1 %RANDOM
Rwork0.1952 ---
obs0.1961 51501 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.536 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20.26 Å2
2---0.29 Å20 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 1.72→63.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 0 15 212 3742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193601
X-RAY DIFFRACTIONr_bond_other_d0.0010.023538
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9744846
X-RAY DIFFRACTIONr_angle_other_deg0.8638162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7985421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64124.253174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97715703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5561522
X-RAY DIFFRACTIONr_chiral_restr0.1030.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02817
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8291.9291690
X-RAY DIFFRACTIONr_mcbond_other1.8091.9281689
X-RAY DIFFRACTIONr_mcangle_it2.6332.8882109
X-RAY DIFFRACTIONr_mcangle_other2.6342.8882110
X-RAY DIFFRACTIONr_scbond_it3.1252.371911
X-RAY DIFFRACTIONr_scbond_other3.1232.361900
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9253.382720
X-RAY DIFFRACTIONr_long_range_B_refined6.11616.3294445
X-RAY DIFFRACTIONr_long_range_B_other6.06916.1454387
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 72 -
Rwork0.212 2625 -
obs--66.56 %

+
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