[English] 日本語
Yorodumi
- PDB-8ch4: Crystal structure of the ring cleaving dioxygenase 5-nitrosalicyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ch4
TitleCrystal structure of the ring cleaving dioxygenase 5-nitrosalicylate 1,2-dioxygenase from Bradyrhizobium sp.
Components5-nitrosalicylic acid 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / oxidase / cupin fold / beta-barrel
Function / homology5-nitrosalicylate dioxygenase / : / Cupin 2, conserved barrel / Cupin domain / dioxygenase activity / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / : / 5-nitrosalicylic acid 1,2-dioxygenase
Function and homology information
Biological speciesBradyrhizobium sp. JS329 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFerraroni, M. / Stolz, A. / Eppinger, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Crystal structure of the monocupin ring-cleaving dioxygenase 5-nitrosalicylate 1,2-dioxygenase from Bradyrhizobium sp.
Authors: Eppinger, E. / Stolz, A. / Ferraroni, M.
History
DepositionFeb 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5-nitrosalicylic acid 1,2-dioxygenase
B: 5-nitrosalicylic acid 1,2-dioxygenase
C: 5-nitrosalicylic acid 1,2-dioxygenase
D: 5-nitrosalicylic acid 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4878
Polymers95,2644
Non-polymers2234
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21220 Å2
ΔGint-218 kcal/mol
Surface area26600 Å2
Unit cell
Length a, b, c (Å)50.427, 143.173, 60.076
Angle α, β, γ (deg.)90.00, 107.33, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
5-nitrosalicylic acid 1,2-dioxygenase / 5NSA 1 / 2-dioxygenase / 5-nitroanthranilic acid degradation protein B


Mass: 23816.018 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. JS329 (bacteria) / Gene: naaB / Plasmid: pJS804 / Production host: Escherichia coli (E. coli) / References: UniProt: D3WZ86, 5-nitrosalicylate dioxygenase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% MPD, 5% PEG 400, 100 mM TRIS-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2019 / Details: LN2 closed loop cooling
RadiationMonochromator: Double Crystal Manochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.14 Å / Num. obs: 46889 / % possible obs: 99.2 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.18 / Net I/σ(I): 9.09
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.1-2.231.58774650.6821.7221
2.23-2.381.14870770.7931.2411
2.38-2.570.76466270.8920.8271
2.57-2.820.45661090.9650.4931
2.82-3.150.2455600.9890.261
3.15-3.630.12248730.9960.1321
3.63-4.440.0741470.9980.0761
4.44-6.260.05732220.9980.0621
6.26-48.140.03918090.9990.0431

-
Processing

Software
NameVersionClassification
REFMAC5.8refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU B: 13.09 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27642 2241 4.8 %RANDOM
Rwork0.21617 ---
obs0.21899 44632 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.508 Å2
Baniso -1Baniso -2Baniso -3
1-5.31 Å2-0 Å22.63 Å2
2---4.88 Å20 Å2
3----1.74 Å2
Refinement stepCycle: 1 / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5689 0 4 157 5850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125857
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.6287960
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8115723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67322.628293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10515907
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7171525
X-RAY DIFFRACTIONr_chiral_restr0.1010.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024505
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.1974.5962898
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.716.8813616
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2584.7522959
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.45862.5959377
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 150 -
Rwork0.416 3222 -
obs--97.88 %

+
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