[English] 日本語
Yorodumi
- PDB-5dz6: Acyl transferase from Bacillaene PKS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dz6
TitleAcyl transferase from Bacillaene PKS
ComponentsPolyketide biosynthesis malonyl CoA-acyl carrier protein transacylase PksC
KeywordsTRANSFERASE / polyketide synthase / acyltrasferase
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / cytosol
Similarity search - Function
Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / : / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / : / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / DI(HYDROXYETHYL)ETHER / Polyketide biosynthesis malonyl CoA-acyl carrier protein transacylase PksC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsTill, M. / Race, P.R.
Citation
Journal: To Be Published
Title: Architectural hierarchy of trans-acting enoyl reductases from polyunsaturated fatty acid and trans-acyltransferase polyketide synthases
Authors: Till, M. / Burton, N.J. / Akrill, T.D. / van der Kamp, M.W. / Baker, G.E. / Byrne, M.J. / Owen, R.L. / Willis, C.L. / Race, P.R.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2011
Title: Crystallization and preliminary X-ray analysis of the bacillaene synthase trans-acting acyltransferase PksC.
Authors: Cuskin, F. / Solovyova, A.S. / Lewis, R.J. / Race, P.R.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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: Polyketide biosynthesis malonyl CoA-acyl carrier protein transacylase PksC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9398
Polymers32,4481
Non-polymers4917
Water5,459303
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-18 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.190, 70.430, 76.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Polyketide biosynthesis malonyl CoA-acyl carrier protein transacylase PksC / AT


Mass: 32448.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: pksC, BSU17100 / Production host: Escherichia coli (E. coli)
References: UniProt: O34825, [acyl-carrier-protein] S-malonyltransferase

-
Non-polymers , 6 types, 310 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, 0.2M sodium bromide, 0.1M bistris propane pH 9.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9699 Å / Relative weight: 1
ReflectionResolution: 1.44→37.09 Å / Num. all: 71820 / Num. obs: 51033 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.6
Reflection shellResolution: 1.44→1.51 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.306 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3g87

3g87


Resolution: 1.44→37.09 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.2009 / WRfactor Rwork: 0.1769 / FOM work R set: 0.9072 / SU B: 0.876 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0626 / SU Rfree: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 2686 5.1 %RANDOM
Rwork0.1627 ---
obs0.1638 50147 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.51 Å2 / Biso mean: 12.465 Å2 / Biso min: 2.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0 Å20 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 1.44→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 21 306 2608
Biso mean--20.32 21.73 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022471
X-RAY DIFFRACTIONr_angle_refined_deg2.5451.9773350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1775322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60825.31113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6615463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.044157
X-RAY DIFFRACTIONr_chiral_restr0.1590.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211875
LS refinement shellResolution: 1.436→1.473 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 192 -
Rwork0.223 3430 -
all-3622 -
obs--99.48 %

+
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