[English] 日本語
Yorodumi
- PDB-7r9x: Crystal structure of a dehydrating condensation domain, AmbE-Cmod... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r9x
TitleCrystal structure of a dehydrating condensation domain, AmbE-CmodAA, involved in nonribosomal peptide synthesis
ComponentsAmbE
KeywordsBIOSYNTHETIC PROTEIN / Condensation domain Nonribosomal peptide synthetases (NRPSs)
Function / homology
Function and homology information


L-glutamate-[L-glutamyl-carrier protein] ligase / amide biosynthetic process / : / secondary metabolite biosynthetic process / phosphopantetheine binding / catalytic activity
Similarity search - Function
Methyltransferase FkbM / Methyltransferase FkbM domain / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain ...Methyltransferase FkbM / Methyltransferase FkbM domain / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
IODIDE ION / AMB antimetabolite synthase AmbE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsFortinez, C.M. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-148472 Canada
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Structure and Function of a Dehydrating Condensation Domain in Nonribosomal Peptide Biosynthesis.
Authors: Patteson, J.B. / Fortinez, C.M. / Putz, A.T. / Rodriguez-Rivas, J. / Bryant 3rd, L.H. / Adhikari, K. / Weigt, M. / Schmeing, T.M. / Li, B.
History
DepositionJun 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: 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
Revision 1.2Aug 24, 2022Group: 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 1.3Oct 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: AmbE
B: AmbE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,88319
Polymers95,9722
Non-polymers91017
Water9,134507
1
A: AmbE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,50510
Polymers47,9861
Non-polymers5199
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AmbE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3789
Polymers47,9861
Non-polymers3928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.940, 106.870, 108.909
Angle α, β, γ (deg.)90.000, 96.252, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

-
Components

#1: Protein AmbE


Mass: 47986.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ambE, PA2302 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I1H3
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: AmbE_Cd crystallized at a concentration of 10mg/ml in conditions containing 100mM bis-Tris propane (pH 6.0), 20% PEG3350 and 0.2M sodium iodide. Cryoprotection was performed by dipping the ...Details: AmbE_Cd crystallized at a concentration of 10mg/ml in conditions containing 100mM bis-Tris propane (pH 6.0), 20% PEG3350 and 0.2M sodium iodide. Cryoprotection was performed by dipping the crystal in a solution containing 20% MPD (hexylene glycol), 0.2M NaCl, 50mM Tris-Cl (pH7.5), 0.2M sodium iodide, 20% PEG 3350 and 100mM bis-Tris propane (pH 6.0) before being flash frozen in liquid nitrogen.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.14→76.06 Å / Num. obs: 55789 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.49 Å2 / CC1/2: 0.987 / Net I/σ(I): 16.2
Reflection shellResolution: 2.14→2.2 Å / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 55789 / CC1/2: 0.89

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JGP, 6OYF

2jgp

6oyf


Resolution: 2.14→44.7 Å / SU ML: 0.2313 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3897
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2323 2000 3.58 %
Rwork0.1896 53789 -
obs0.1912 55789 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.19 Å2
Refinement stepCycle: LAST / Resolution: 2.14→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6348 0 17 510 6875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116481
X-RAY DIFFRACTIONf_angle_d1.1238810
X-RAY DIFFRACTIONf_chiral_restr0.0581985
X-RAY DIFFRACTIONf_plane_restr0.00691171
X-RAY DIFFRACTIONf_dihedral_angle_d21.88092357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.20.2371440.19233852X-RAY DIFFRACTION99.65
2.2-2.250.27731420.19593849X-RAY DIFFRACTION99.6
2.25-2.320.26451430.20553853X-RAY DIFFRACTION99.7
2.32-2.40.22961420.23810X-RAY DIFFRACTION99.75
2.4-2.480.24141440.19323859X-RAY DIFFRACTION99.6
2.48-2.580.24031420.19623830X-RAY DIFFRACTION98.83
2.58-2.70.25221390.23723X-RAY DIFFRACTION96.74
2.7-2.840.26371440.2043876X-RAY DIFFRACTION99.78
2.84-3.020.26471430.20683842X-RAY DIFFRACTION99.55
3.02-3.250.24661430.20283869X-RAY DIFFRACTION99.75
3.25-3.580.21261440.17473858X-RAY DIFFRACTION99.4
3.58-4.10.22041400.1653774X-RAY DIFFRACTION97.1
4.1-5.160.19191440.16013890X-RAY DIFFRACTION99.95
5.16-44.70.23571460.21743904X-RAY DIFFRACTION98.47

+
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://pdbjlvh1.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