[English] 日本語
Yorodumi
- PDB-7jsd: Hydroxylase homolog of BesD with Fe(II), alpha-ketoglutarate, and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jsd
TitleHydroxylase homolog of BesD with Fe(II), alpha-ketoglutarate, and lysine
ComponentsLysine hydroxylase
KeywordsBIOSYNTHETIC PROTEIN / Hydroxylase / non-heme iron
Function / homology2-OXOGLUTARIC ACID / : / LYSINE
Function and homology information
Biological speciesStreptomyces roseifaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKissman, E.N. / Neugebauer, M.E. / Chang, M.C.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)LBNL DEAC02-05CH11231, FWP CH030201 United States
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Reaction pathway engineering converts a radical hydroxylase into a halogenase.
Authors: Neugebauer, M.E. / Kissman, E.N. / Marchand, J.A. / Pelton, J.G. / Sambold, N.A. / Millar, D.C. / Chang, M.C.Y.
History
DepositionAug 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine hydroxylase
B: Lysine hydroxylase
C: Lysine hydroxylase
D: Lysine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,95317
Polymers120,3154
Non-polymers1,63813
Water7,260403
1
A: Lysine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6225
Polymers30,0791
Non-polymers5434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6225
Polymers30,0791
Non-polymers5434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4284
Polymers30,0791
Non-polymers3493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2813
Polymers30,0791
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.626, 93.530, 91.339
Angle α, β, γ (deg.)90.000, 107.560, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Lysine hydroxylase


Mass: 30078.697 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces roseifaciens (bacteria) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 5 types, 416 molecules

#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: In an anaerobic chamber, equal volumes of protein solution (3 mg/mL Hydroxylase, lysine (3 mM), KG (3 mM, pH 7)) and reservoir solution (HEPES pH 7.0 (100 mM), sodium nitrate (200 mM) ...Details: In an anaerobic chamber, equal volumes of protein solution (3 mg/mL Hydroxylase, lysine (3 mM), KG (3 mM, pH 7)) and reservoir solution (HEPES pH 7.0 (100 mM), sodium nitrate (200 mM) containing 28% (w/v) PEG 3350); Crystals were soaked with iron chloride before flash freezing

-
Data collection

DiffractionMean temperature: 194 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.111 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.111 Å / Relative weight: 1
ReflectionResolution: 2.5→87.081 Å / Num. obs: 40203 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 38.69 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.253 / Rrim(I) all: 0.2744 / Net I/σ(I): 6.2
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 1.644 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 3972 / CC1/2: 0.519 / CC star: 0.827

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NIE

6nie


Resolution: 2.5→87.08 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1967 4.89 %
Rwork0.1802 38233 -
obs0.1826 40200 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.85 Å2 / Biso mean: 43.7164 Å2 / Biso min: 13.89 Å2
Refinement stepCycle: final / Resolution: 2.5→87.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7831 0 100 403 8334
Biso mean--43.56 43.84 -
Num. residues----989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0018110
X-RAY DIFFRACTIONf_angle_d0.43411021
X-RAY DIFFRACTIONf_dihedral_angle_d13.234834
X-RAY DIFFRACTIONf_chiral_restr0.0411237
X-RAY DIFFRACTIONf_plane_restr0.0031438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.56260.30461290.2546270799
2.5626-2.63190.32031390.2445269199
2.6319-2.70930.30521260.2355272899
2.7093-2.79680.30481320.2323271699
2.7968-2.89670.3191470.2255273099
2.8967-3.01270.26461450.1961269599
3.0127-3.14980.26121280.20282742100
3.1498-3.31590.25081640.18942680100
3.3159-3.52370.24771440.1741272899
3.5237-3.79570.17681400.15762746100
3.7957-4.17770.19231370.14582734100
4.1777-4.78220.19531470.13532755100
4.7822-6.02480.20071480.17392762100
6.0248-87.080.19541410.18432819100

+
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