[English] 日本語
Yorodumi
- PDB-7agu: Structure of the S726F mutant of AcylTransferase domain of Mycoce... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7agu
TitleStructure of the S726F mutant of AcylTransferase domain of Mycocerosic Acid Synthase from Mycobacterium tuberculosis acylated with MethylMalonyl-coenzyme A
ComponentsMycocerosic acid synthase
KeywordsTRANSFERASE / Mycocerosic Acid Synthase / AcylTransferase domain / polyketide synthase / Mycobacterium tuberculosis / methylmalonyl-coenzyme A
Function / homology
Function and homology information


mycocerosate synthase / mycocerosate synthase activity / phosphopantetheine binding / ligase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / hydrolase activity / plasma membrane
Similarity search - Function
Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / : / Polyketide synthase dehydratase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain ...Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / : / Polyketide synthase dehydratase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Ketosynthase family 3 (KS3) domain profile. / 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 / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
METHYLMALONIC ACID / Mycocerosic acid synthase
Similarity search - Component
Biological speciesMycobacterium bovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å
AuthorsBrison, Y. / Mourey, L. / Maveyraud, L.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-09-BLAN-0298-01 France
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Molecular Basis for Extender Unit Specificity of Mycobacterial Polyketide Synthases.
Authors: Grabowska, A.D. / Brison, Y. / Maveyraud, L. / Gavalda, S. / Faille, A. / Nahoum, V. / Bon, C. / Guilhot, C. / Pedelacq, J.D. / Chalut, C. / Mourey, L.
History
DepositionSep 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: 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 1.2Jul 14, 2021Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mycocerosic acid synthase
B: Mycocerosic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2414
Polymers93,0612
Non-polymers1802
Water57632
1
A: Mycocerosic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6492
Polymers46,5311
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mycocerosic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5932
Polymers46,5311
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.15, 157.975, 116.299
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Mycocerosic acid synthase


Mass: 46530.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) (bacteria)
Strain: ATCC BAA-935 / AF2122/97 / Gene: mas, BQ2027_MB2965C / Production host: Escherichia coli (E. coli) / References: UniProt: Q02251, mycocerosate synthase
#2: Chemical ChemComp-DXX / METHYLMALONIC ACID / Methylmalonic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 1.1 M sodium succinate 0.1 M sodium acetate buffer

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.1→47.13 Å / Num. obs: 25082 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 118.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.099 / Rsym value: 0.091 / Net I/σ(I): 14.3
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.511 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3968 / CC1/2: 0.542 / Rrim(I) all: 1.648 / Rsym value: 1.511 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
REFMAC5.8.0258refinement
XDSdata processing
Cootmodel building
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7AGP

7agp


Resolution: 3.1→47.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / SU R Blow DPI: 13.31 / SU Rfree Blow DPI: 0.316
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 1229 -RANDOM
Rwork0.183 ---
obs0.1843 25082 99.9 %-
Displacement parametersBiso mean: 125.71 Å2
Baniso -1Baniso -2Baniso -3
1--23.2193 Å20 Å20 Å2
2--5.8948 Å20 Å2
3---17.3244 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 3.1→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6303 0 11 32 6346
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116450HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.098819HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2133SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1118HARMONIC5
X-RAY DIFFRACTIONt_it6445HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion864SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4923SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion18.68
LS refinement shellResolution: 3.1→3.12 Å
RfactorNum. reflection% reflection
Rfree0.2887 15 -
Rwork0.3526 --
obs0.3507 502 94.84 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8045-2.2844-0.44354.6073-1.04171.9626-0.10780.16780.19010.16780.0654-0.05610.1901-0.05610.04240.34730.2152-0.02040.3938-0.02730.224830.4107-29.1462-7.1393
23.0235-1.5921-1.20122.49670.9293.6886-0.16430.3674-0.1250.3674-0.1181-0.5548-0.125-0.55480.28240.34350.0822-0.05630.1428-0.04860.1867-30.499417.002212.2905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|445 - A|901 }A445 - 871
2X-RAY DIFFRACTION1{ A|445 - A|901 }A901
3X-RAY DIFFRACTION2{ B|445 - B|901 }B445 - 871
4X-RAY DIFFRACTION2{ B|445 - B|901 }B901

+
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