[English] 日本語
Yorodumi
- PDB-5l84: Structure of the H959F variant of the PpsC dehydratase domain fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l84
TitleStructure of the H959F variant of the PpsC dehydratase domain from Mycobacterium tuberculosis
ComponentsPhthiocerol synthesis polyketide synthase type I PpsC
KeywordsTRANSFERASE / dehydratase / polyketide / complex / tuberculosis
Function / homology
Function and homology information


(phenol)carboxyphthiodiolenone synthase / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / Actinobacterium-type cell wall biogenesis / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process ...(phenol)carboxyphthiodiolenone synthase / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / Actinobacterium-type cell wall biogenesis / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Polyketide synthase dehydratase / : / Zinc-binding dehydrogenase / : / 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 dehydratase / : / Zinc-binding dehydrogenase / : / 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 / Malonyl-CoA ACP transacylase, ACP-binding / Thiol Ester Dehydrase; Chain A / 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, 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 / Phosphopantetheine attachment site. / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Phenolphthiocerol/phthiocerol polyketide synthase subunit C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFaille, A. / Gavalda, S. / Mourey, L. / Pedelacq, J.D.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency09-BLAN-0298-01 France
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Insights into Substrate Modification by Dehydratases from Type I Polyketide Synthases.
Authors: Faille, A. / Gavalda, S. / Slama, N. / Lherbet, C. / Maveyraud, L. / Guillet, V. / Laval, F. / Quemard, A. / Mourey, L. / Pedelacq, J.D.
History
DepositionJun 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 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: Phthiocerol synthesis polyketide synthase type I PpsC


Theoretical massNumber of molelcules
Total (without water)34,4681
Polymers34,4681
Non-polymers00
Water0
1
A: Phthiocerol synthesis polyketide synthase type I PpsC

A: Phthiocerol synthesis polyketide synthase type I PpsC


Theoretical massNumber of molelcules
Total (without water)68,9372
Polymers68,9372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1350 Å2
ΔGint-10 kcal/mol
Surface area23680 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.787, 83.787, 165.754
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Phthiocerol synthesis polyketide synthase type I PpsC / Beta-ketoacyl-acyl-carrier-protein synthase I


Mass: 34468.465 Da / Num. of mol.: 1 / Mutation: H959F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: ppsC, Rv2933 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P96202, beta-ketoacyl-[acyl-carrier-protein] synthase I

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.68 Å3/Da / Density % sol: 73.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Na/K PO4 1.8 M pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.9→46.125 Å / Num. obs: 13660 / % possible obs: 99 % / Redundancy: 10.47 % / Net I/σ(I): 18.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OOC

4ooc


Resolution: 2.9→48.197 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 1279 9.39 %
Rwork0.1922 12346 -
obs0.1947 13625 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 260.48 Å2 / Biso mean: 95.2682 Å2 / Biso min: 33.39 Å2
Refinement stepCycle: final / Resolution: 2.9→48.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 0 0 2004
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042036
X-RAY DIFFRACTIONf_angle_d0.8562785
X-RAY DIFFRACTIONf_chiral_restr0.032341
X-RAY DIFFRACTIONf_plane_restr0.004365
X-RAY DIFFRACTIONf_dihedral_angle_d16.049720
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9001-3.01620.34051390.344713431482100
3.0162-3.15350.36391380.304513311469100
3.1535-3.31970.32811390.27661357149699
3.3197-3.52760.27911380.23611346148499
3.5276-3.79990.24351420.214613551497100
3.7999-4.18210.19971410.178313631504100
4.1821-4.78680.17761430.13513771520100
4.7868-6.0290.16841460.1631403154999
6.029-48.2040.19291530.17161471162498
Refinement TLS params.

Method: refined / 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)
10.94160.5076-0.44880.44890.10210.60040.13760.3849-0.09480.1814-0.0674-0.06160.2647-0.01660.01880.4211-0.0878-0.02220.55780.04450.490592.6053107.76759.5077
22.7544-1.3607-2.57220.69841.26242.33210.247-0.1739-0.0284-0.1806-0.0129-0.02040.29960.28230.00010.64970.0077-0.06660.47840.0640.498398.4161110.575315.5212
30.15740.37150.15780.82250.34750.1343-0.06320.0884-0.7194-0.22570.3941-0.2241-0.1639-0.0646-0.00020.43940.05830.00210.5874-0.02230.5181102.8446111.21359.2838
40.96180.1158-0.21150.50010.11710.08260.38580.54990.44990.0066-0.19850.30340.38351.104-0.00240.63610.08390.06390.7113-0.01650.643299.9262114.50576.8644
50.0985-0.2066-0.22320.26410.47740.50440.2480.07250.01730.02060.04080.4034-0.3140.0720.00180.67920.21280.04460.86540.19430.449482.2907119.518134.6151
60.27420.12560.32620.78840.28460.4330.06150.01760.33360.11270.2259-0.11340.2466-1.24380.11330.69580.14440.24270.87980.19060.623476.8141116.743623.0164
70.73790.5727-0.63380.7979-0.65680.5896-0.4488-0.4444-0.2322-0.0818-0.02370.49390.29380.3711-0.0080.7823-0.01740.18410.4690.03990.541984.6539108.800426.9844
80.5544-1.3427-0.66143.19151.4621.5301-0.379-0.27020.40570.62980.95720.7510.454-0.00390.48960.43930.03280.15720.29770.03320.704683.9425121.930525.9345
91.7134-0.5117-0.0640.1945-0.14360.35710.2827-0.40230.14320.38650.00270.2720.14670.353200.72590.00140.04210.5620.02020.608592.0997114.513227.5717
100.4143-0.00240.2066-0.0019-0.00980.09170.3096-1.08410.29950.5718-0.5564-0.1410.19910.8245-0.02250.7618-0.0430.05710.6058-0.05450.781992.6291123.83128.8464
111.1281-0.7087-0.47720.55580.50890.530.2718-0.67020.19480.66560.48980.2712-0.44950.03760.07190.88880.05850.06450.65710.04610.779992.2809117.724927.7532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 926 through 981 )A926 - 981
2X-RAY DIFFRACTION2chain 'A' and (resid 982 through 1008 )A982 - 1008
3X-RAY DIFFRACTION3chain 'A' and (resid 1009 through 1029 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1030 through 1045 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1046 through 1078 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1079 through 1098 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1099 through 1124 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1125 through 1160 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1161 through 1185 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 1186 through 1200 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 1201 through 1218 )A0

+
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