[English] 日本語
Yorodumi
- PDB-8fhb: Protein 32 with aldehyde deformylating oxidase activity from Syne... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fhb
TitleProtein 32 with aldehyde deformylating oxidase activity from Synechococcus sp.
ComponentstRNA-(MS[2]IO[6]A)-hydroxylase
KeywordsLYASE / aldehyde deformylating oxygenase
Function / homologytRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity / tRNA-hydroxylase MiaE / tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE) / tRNA modification / Ferritin-like / Ferritin-like superfamily / metal ion binding / : / tRNA-(MS[2]IO[6]A)-hydroxylase
Function and homology information
Biological speciesSynechococcus sp. RCC307 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsArenas, R. / Wilson, D.K. / Mak, W.S. / Siegel, J.B.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Protein 32 with aldehyde deformylating oxidase activity from Synechococcus sp.
Authors: Arenas, R. / Wilson, D.K. / Mak, W.S. / Siegel, J.B.
History
DepositionDec 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA-(MS[2]IO[6]A)-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8362
Polymers25,7801
Non-polymers561
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.192, 74.330, 111.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein tRNA-(MS[2]IO[6]A)-hydroxylase


Mass: 25780.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. RCC307 (bacteria) / Gene: miaE / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A5GR51
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4,000, 200 mM MgCl2, 100 mM HEPES HCl

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.95→37.32 Å / Num. obs: 17168 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 27.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.017 / Rrim(I) all: 0.061 / Net I/σ(I): 26.7
Reflection shellResolution: 1.95→2 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1177 / CC1/2: 0.937 / Rpim(I) all: 0.186 / Rrim(I) all: 0.692 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→37.165 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.465 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 826 4.818 %0.05
Rwork0.1692 16317 --
all0.172 ---
obs-17143 99.901 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.558 Å2
Baniso -1Baniso -2Baniso -3
1-0.004 Å20 Å20 Å2
2--0.018 Å20 Å2
3----0.022 Å2
Refinement stepCycle: LAST / Resolution: 1.95→37.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 1 85 1700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161531
X-RAY DIFFRACTIONr_angle_refined_deg2.1171.6442244
X-RAY DIFFRACTIONr_angle_other_deg0.7271.5533563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0135203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.147519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20110277
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.0681079
X-RAY DIFFRACTIONr_chiral_restr0.1110.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02322
X-RAY DIFFRACTIONr_nbd_refined0.2340.2355
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21346
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2805
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2884
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.262
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.211
X-RAY DIFFRACTIONr_nbd_other0.1810.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.214
X-RAY DIFFRACTIONr_mcbond_it4.293.477815
X-RAY DIFFRACTIONr_mcbond_other4.2883.477815
X-RAY DIFFRACTIONr_mcangle_it5.5715.1921017
X-RAY DIFFRACTIONr_mcangle_other5.5695.1961018
X-RAY DIFFRACTIONr_scbond_it5.7784.058836
X-RAY DIFFRACTIONr_scbond_other5.7744.062837
X-RAY DIFFRACTIONr_scangle_it7.7615.8631227
X-RAY DIFFRACTIONr_scangle_other7.7585.8671228
X-RAY DIFFRACTIONr_lrange_it8.90145.1421852
X-RAY DIFFRACTIONr_lrange_other8.89445.1051847
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.95-2.0010.256690.25211660.25212360.9410.95199.91910.206
2.001-2.0550.255480.21611580.21812060.9340.9681000.18
2.055-2.1150.225550.19411500.19512050.9690.9751000.168
2.115-2.1790.261530.18110710.18411250.9580.9899.91110.152
2.179-2.2510.234530.17210610.17511160.9660.98299.82080.145
2.251-2.3290.204460.17310600.17511080.9740.98199.81950.156
2.329-2.4170.256540.1639740.16810280.9620.9831000.142
2.417-2.5150.213410.1719670.17210090.9680.98299.90090.151
2.515-2.6270.232460.1589210.1619670.9740.9861000.14
2.627-2.7540.219430.1758890.1779350.9740.98399.67910.157
2.754-2.9020.305410.1868450.1928860.9550.9791000.17
2.902-3.0770.214510.1997850.28360.9710.9741000.184
3.077-3.2880.25420.1867500.1897920.9610.9791000.176
3.288-3.5490.236300.1617120.1637430.9630.98599.86540.158
3.549-3.8840.194330.1536510.1556850.9730.98899.8540.153
3.884-4.3370.192310.1435870.1456180.9830.9881000.145
4.337-4.9960.203330.1435250.1475580.9760.9891000.147
4.996-6.0920.182240.1914540.194790.9890.98499.79120.195
6.092-8.5010.173170.1383620.143800.9870.98699.73680.14
8.501-37.1650.178160.172290.1712450.9640.981000.198

+
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