[English] 日本語
Yorodumi
- PDB-6x7p: LnmK in complex with 2-sulfonate-propionyl-oxa(dethia)-CoA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x7p
TitleLnmK in complex with 2-sulfonate-propionyl-oxa(dethia)-CoA
ComponentsConserved hypthetical protein
Keywordstransferase/transferase inhibitor / transferase / lyase / inhibitor / isostere / transferase-transferase inhibitor complex
Function / homology
Function and homology information


S-acyltransferase activity
Similarity search - Function
: / LnmK, N-terminal / LnmK N-terminal Hot Dog Fold domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-LCV / Chem-SO5 / Conserved hypthetical protein
Similarity search - Component
Biological speciesStreptomyces atroolivaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsStunkard, L.M. / Kick, B.J. / Lohman, J.R.
CitationJournal: Biochemistry / Year: 2021
Title: Structures of LnmK, a Bifunctional Acyltransferase/Decarboxylase, with Substrate Analogues Reveal the Basis for Selectivity and Stereospecificity.
Authors: Stunkard, L.M. / Kick, B.J. / Lohman, J.R.
History
DepositionMay 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Conserved hypthetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6368
Polymers35,3801
Non-polymers2,2567
Water4,954275
1
A: Conserved hypthetical protein
hetero molecules

A: Conserved hypthetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,27216
Polymers70,7612
Non-polymers4,51114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area5450 Å2
ΔGint-163 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.087, 61.087, 312.986
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-407-

SO4

-
Components

#1: Protein Conserved hypthetical protein


Mass: 35380.387 Da / Num. of mol.: 1 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces atroolivaceus (bacteria) / Gene: LnmK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8GGP1
#2: Chemical ChemComp-SO5 / (2~{R})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid


Mass: 887.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40N7O21P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LCV / (2~{S})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid


Mass: 887.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40N7O21P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 9% PEG400, 100 mM Bis-Tris pH 7.5, 28% PEG3350 / Temp details: room temperature

-
Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 17, 2016 / Details: MD2 microdifractometer
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 51370 / % possible obs: 99.1 % / Redundancy: 17.9 % / Biso Wilson estimate: 32.29 Å2 / Rmerge(I) obs: 0.261 / Rsym value: 0.288 / Net I/σ(I): 91.9
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4621 / Rsym value: 1 / % possible all: 91.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZO

4hzo


Resolution: 1.55→47.23 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.787 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2589 5.1 %RANDOM
Rwork0.179 ---
obs0.181 48639 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.55→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 117 275 2769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132670
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172350
X-RAY DIFFRACTIONr_angle_refined_deg2.2291.7253666
X-RAY DIFFRACTIONr_angle_other_deg1.4831.6335421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6055320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29219.873157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76615382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2021531
X-RAY DIFFRACTIONr_chiral_restr0.2650.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022992
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02615
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 163 -
Rwork0.341 3352 -
obs--95.52 %

+
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