[English] 日本語
Yorodumi
- PDB-9dk3: Lexapeptide dehydratase complex LxmKY, hydrolysed ATP bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dk3
TitleLexapeptide dehydratase complex LxmKY, hydrolysed ATP bound
Components
  • Kinase
  • Lyase
KeywordsBIOSYNTHETIC PROTEIN / Kinase / Lyase / lanthipeptide dehydratase / complex
Function / homology
Function and homology information


HopA1 effector protein / HopA1 effector protein family / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ACETIC ACID / ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Aminoglycoside phosphotransferase domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesStreptomyces rochei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRandall, G.T. / Bashiri, G.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Marsden Fund New Zealand
Other privateAuckland Medical Research Foundation
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: A Stable Dehydratase Complex Catalyzes the Formation of Dehydrated Amino Acids in a Class V Lanthipeptide.
Authors: Randall, G.T. / Grant-Mackie, E.S. / Chunkath, S. / Williams, E.T. / Middleditch, M.J. / Tao, M. / Harris, P.W.R. / Brimble, M.A. / Bashiri, G.
History
DepositionSep 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kinase
B: Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,76514
Polymers82,5592
Non-polymers1,20512
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-58 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.175, 91.583, 151.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Kinase


Mass: 43102.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal GA from proteolysed purification tag / Source: (gene. exp.) Streptomyces rochei (bacteria) / Gene: lxmK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K1TP15
#2: Protein Lyase


Mass: 39457.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal GA scar from proteolysed purification tag
Source: (gene. exp.) Streptomyces rochei (bacteria) / Gene: lxmY / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K1TP21

-
Non-polymers , 8 types, 105 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium acetate trihydrate 0.1 M Bis-Tris propane 7.5 20 % w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.3→49.11 Å / Num. obs: 36800 / % possible obs: 100 % / Redundancy: 27.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.458 / Rpim(I) all: 0.125 / Rrim(I) all: 0.475 / Net I/σ(I): 8.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 28.2 % / Num. unique obs: 4216 / CC1/2: 0.41 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
XDSdata reduction
Aimless1.12.13data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.753 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: FREE R-VALUE / ESU R: 0.281 / ESU R Free: 0.227
RfactorNum. reflection% reflection
Rfree0.2571 1804 4.911 %
Rwork0.2083 34930 -
all0.211 --
obs-36734 99.978 %
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: 61.266 Å2
Baniso -1Baniso -2Baniso -3
1--0.657 Å20 Å20 Å2
2--2.016 Å2-0 Å2
3----1.359 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4802 0 74 93 4969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0125005
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164540
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.6396822
X-RAY DIFFRACTIONr_angle_other_deg0.8081.54810485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.0921058
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7810676
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.07310203
X-RAY DIFFRACTIONr_chiral_restr0.0680.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025908
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021001
X-RAY DIFFRACTIONr_nbd_refined0.2180.21063
X-RAY DIFFRACTIONr_symmetry_nbd_other0.230.24017
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22453
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2126
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.210
X-RAY DIFFRACTIONr_nbd_other0.2290.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3670.210
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0930.22
X-RAY DIFFRACTIONr_mcbond_it6.3096.4782619
X-RAY DIFFRACTIONr_mcbond_other6.2786.4782617
X-RAY DIFFRACTIONr_mcangle_it8.8529.7013260
X-RAY DIFFRACTIONr_mcangle_other8.8529.7033261
X-RAY DIFFRACTIONr_scbond_it6.9576.7212386
X-RAY DIFFRACTIONr_scbond_other6.9066.7122383
X-RAY DIFFRACTIONr_scangle_it9.669.9383560
X-RAY DIFFRACTIONr_scangle_other9.5889.9263555
X-RAY DIFFRACTIONr_lrange_it12.02385.9365374
X-RAY DIFFRACTIONr_lrange_other12.02485.9425373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3621330.342546X-RAY DIFFRACTION100
2.36-2.4240.3721180.3242484X-RAY DIFFRACTION100
2.424-2.4940.3281010.2852397X-RAY DIFFRACTION100
2.494-2.5710.3431380.2672334X-RAY DIFFRACTION99.9596
2.571-2.6550.3521240.2552281X-RAY DIFFRACTION100
2.655-2.7480.331010.2382198X-RAY DIFFRACTION99.9565
2.748-2.8510.3051210.2322124X-RAY DIFFRACTION100
2.851-2.9670.275940.2192045X-RAY DIFFRACTION100
2.967-3.0980.2621110.2041978X-RAY DIFFRACTION100
3.098-3.2490.2671130.1991864X-RAY DIFFRACTION100
3.249-3.4240.205940.1751802X-RAY DIFFRACTION100
3.424-3.630.238930.1961708X-RAY DIFFRACTION100
3.63-3.8790.235810.1771625X-RAY DIFFRACTION99.9414
3.879-4.1870.239740.1831500X-RAY DIFFRACTION100
4.187-4.5830.239650.1791399X-RAY DIFFRACTION100
4.583-5.1180.245600.1891273X-RAY DIFFRACTION100
5.118-5.8980.384550.2351141X-RAY DIFFRACTION100
5.898-7.1950.238540.213977X-RAY DIFFRACTION100
7.195-10.0570.18450.171775X-RAY DIFFRACTION100

+
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