[English] 日本語
Yorodumi
- PDB-5ing: A crotonyl-CoA reductase-carboxylase independent pathway for asse... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ing
TitleA crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender unit
ComponentsPutative carboxyl transferase
KeywordsTRANSFERASE / Acyl-CoA / Crotonase / Polyketide / Extender-Unit
Function / homology
Function and homology information


propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / transferase activity
Similarity search - Function
Acetyl-CoA carboxylase carboxyl transferase, beta subunit / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Acetyl-CoA carboxylase carboxyl transferase, beta subunit / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Putative carboxyl transferase
Similarity search - Component
Biological speciesStreptomyces ambofaciens ATCC 23877 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsValentic, T.R. / Ray, L. / Miyazawa, T. / Song, L. / Withall, D.M. / Milligan, J.C. / Takahashi, S. / Osada, H. / Tsai, S.C. / Challis, G.L.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)doctoral training grant United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM100305 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM076330 United States
CitationJournal: Nat Commun / Year: 2016
Title: A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender units.
Authors: Ray, L. / Valentic, T.R. / Miyazawa, T. / Withall, D.M. / Song, L. / Milligan, J.C. / Osada, H. / Takahashi, S. / Tsai, S.C. / Challis, G.L.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative carboxyl transferase
B: Putative carboxyl transferase
C: Putative carboxyl transferase
D: Putative carboxyl transferase
E: Putative carboxyl transferase
F: Putative carboxyl transferase


Theoretical massNumber of molelcules
Total (without water)374,4596
Polymers374,4596
Non-polymers00
Water16,862936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42630 Å2
ΔGint-192 kcal/mol
Surface area94920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.560, 163.440, 186.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Putative carboxyl transferase / Putative propionyl-CoA carboxylase


Mass: 62409.812 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ambofaciens ATCC 23877 (bacteria)
Gene: SAM23877_7108, SAMR0483 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0ACI9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 936 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 6-11% MPD (2-Methyl-2,4-pentanediol), 0.2 M magnesium acetate, and 0.1 M MES pH 6.6-6.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2014
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.45→81.72 Å / Num. obs: 134126 / % possible obs: 99 % / Redundancy: 6.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.112 / Net I/σ(I): 11.8
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 1.6 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXAutoBuildmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IBB

3ibb


Resolution: 2.45→81.72 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 1992 1.49 %
Rwork0.1913 --
obs0.1919 133793 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→81.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22424 0 0 936 23360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722891
X-RAY DIFFRACTIONf_angle_d1.03231107
X-RAY DIFFRACTIONf_dihedral_angle_d15.19913652
X-RAY DIFFRACTIONf_chiral_restr0.0643492
X-RAY DIFFRACTIONf_plane_restr0.0074114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.51130.33011370.27769144X-RAY DIFFRACTION97
2.5113-2.57920.27471390.25369140X-RAY DIFFRACTION97
2.5792-2.65510.27181380.24349143X-RAY DIFFRACTION97
2.6551-2.74080.3061410.23819275X-RAY DIFFRACTION97
2.7408-2.83880.25721400.2279224X-RAY DIFFRACTION98
2.8388-2.95240.30031420.22329393X-RAY DIFFRACTION99
2.9524-3.08680.25441420.20839418X-RAY DIFFRACTION99
3.0868-3.24950.25891440.21049450X-RAY DIFFRACTION100
3.2495-3.45310.23241440.19699515X-RAY DIFFRACTION100
3.4531-3.71980.26821390.19699356X-RAY DIFFRACTION98
3.7198-4.09410.20391420.16949495X-RAY DIFFRACTION99
4.0941-4.68650.17741460.14589605X-RAY DIFFRACTION100
4.6865-5.90420.19381470.16759669X-RAY DIFFRACTION100
5.9042-81.76550.19171510.17619974X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 169.037 Å / Origin y: 5.7567 Å / Origin z: 5.3934 Å
111213212223313233
T0.2327 Å20.0022 Å2-0.0205 Å2-0.1617 Å20.0209 Å2--0.2566 Å2
L0.4006 °20.097 °20.0061 °2-0.4839 °20.3388 °2--1.2025 °2
S0.0495 Å °-0.0273 Å °-0.0724 Å °0.088 Å °-0.0375 Å °-0.0074 Å °0.1748 Å °-0.0148 Å °-0.0039 Å °
Refinement TLS groupSelection details: all

+
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