[English] 日本語
Yorodumi
- PDB-7tzl: The DH dehydratase domain of AlnB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tzl
TitleThe DH dehydratase domain of AlnB
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsLYASE / dehydratase
Function / homology
Function and homology information


: / : / : / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / : / [acyl-carrier-protein] S-acetyltransferase activity / polyketide biosynthetic process / : ...: / : / : / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / : / [acyl-carrier-protein] S-acetyltransferase activity / polyketide biosynthetic process / : / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / Methyltransferase type 12 / Methyltransferase domain / Thioesterase / Thioesterase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...Polyketide synthase, thioesterase domain / Thioesterase / Methyltransferase type 12 / Methyltransferase domain / Thioesterase / Thioesterase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Alcohol dehydrogenase-like, C-terminal / Acyl transferase/acyl hydrolase/lysophospholipase / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Carrier domain-containing protein
Similarity search - Component
Biological speciesStreptomyces griseofuscus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSwain, K. / Blackson, W. / Wang, B. / Zhao, H. / Nannenga, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI144967 United States
CitationJournal: To Be Published
Title: The programming of alpha,beta-polyene biosynthesis by a bacterial iterative type I polyketide synthase
Authors: Wang, B. / Swain, K. / Guo, F. / Blackson, W. / Huang, C. / Chen, B. / Martin, T.A. / Nannenga, B.L. / Zhao, H.
History
DepositionFeb 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)70,5312
Polymers70,5312
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.938, 73.973, 129.905
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 15 through 226 or resid 232 through 292))
21(chain B and resid 15 through 292)

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASPASP(chain A and (resid 15 through 226 or resid 232 through 292))AA15 - 22636 - 247
12LYSLYSSERSER(chain A and (resid 15 through 226 or resid 232 through 292))AA232 - 292253 - 313
21GLYGLYSERSER(chain B and resid 15 through 292)BB15 - 29236 - 313

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999984, -0.000112, -0.005659), (2.6E-5, 0.999701, -0.024464), (0.00566, -0.024464, -0.999685)64.130943, 0.24273, 35.722919

-
Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] synthase / Acyl-[acyl-carrier-protein] hydrolase / Enoyl-[acyl- ...3-oxoacyl-[acyl-carrier-protein] synthase / Acyl-[acyl-carrier-protein] hydrolase / Enoyl-[acyl-carrier-protein] reductase / [Acyl-carrier-protein] S-acetyltransferase / [Acyl-carrier-protein] S-malonyltransferase


Mass: 35265.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseofuscus (bacteria) / Gene: HEP81_06724 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7H1Q9H8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 12 mg/mL, 0.2 M Ammonium Sulfate, 0.1 M Tris pH 6.0, 29% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03316 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 2.35→48.37 Å / Num. obs: 24748 / % possible obs: 94.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 45.56 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Net I/σ(I): 5.8
Reflection shellResolution: 2.35→2.44 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1685 / CC1/2: 0.346 / % possible all: 67.4

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KG8

3kg8


Resolution: 2.45→48.37 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 34.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2877 1154 5.09 %RANDOM
Rwork0.2464 21513 --
obs0.2485 22667 97.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.8 Å2 / Biso mean: 49.7169 Å2 / Biso min: 18.38 Å2
Refinement stepCycle: final / Resolution: 2.45→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4275 0 0 52 4327
Biso mean---49.42 -
Num. residues----542
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1634X-RAY DIFFRACTION4.253TORSIONAL
12B1634X-RAY DIFFRACTION4.253TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.560.42961230.45142224234783
2.56-2.70.34791570.35342661281898
2.7-2.870.35091190.287827422861100
2.87-3.090.30591630.277627302893100
3.09-3.40.28541480.237627272875100
3.4-3.890.29891350.22992756289199
3.89-4.90.22711560.19442782293899
4.9-48.370.27051530.22442891304499

+
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