[English] 日本語
Yorodumi
- PDB-8r2q: Mycobacterium tuberculosis fatty acyl CoA synthetase, FadD5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r2q
TitleMycobacterium tuberculosis fatty acyl CoA synthetase, FadD5
ComponentsProbable fatty-acid-CoA ligase FadD5 (Fatty-acid-CoA synthetase) (Fatty-acid-CoA synthase)
KeywordsLIGASE / FadD5 / Fatty acyl CoA synthetase / Mycobacterium tuberculosis / mce1 operon
Function / homology
Function and homology information


CoA-ligase activity
Similarity search - Function
: / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Probable fatty-acid-CoA ligase FadD5 (Fatty-acid-CoA synthetase) (Fatty-acid-CoA synthase)
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRahman, M.A. / Dalwani, S. / Venkatesan, R.
Funding supportEuropean Union, Finland, 6items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission713606European Union
Academy of Finland332967 Finland
Other privateSigrid Juselius Foundation
Other privateTampere Tuberculosis Foundation
Other governmentUniversity of Oulu
Jane and Aatos Erkko Foundation Finland
CitationJournal: To Be Published
Title: Structural enzymological studies of the long chain fatty acyl-CoA synthetase FadD5 from the mce1 operon of Mycobacterium tuberculosis
Authors: Rahman, M.A. / Dalwani, S. / Venkatesan, R.
History
DepositionNov 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable fatty-acid-CoA ligase FadD5 (Fatty-acid-CoA synthetase) (Fatty-acid-CoA synthase)
B: Probable fatty-acid-CoA ligase FadD5 (Fatty-acid-CoA synthetase) (Fatty-acid-CoA synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,0257
Polymers123,5652
Non-polymers4605
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-22 kcal/mol
Surface area32490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.914, 120.914, 247.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Probable fatty-acid-CoA ligase FadD5 (Fatty-acid-CoA synthetase) (Fatty-acid-CoA synthase)


Mass: 61782.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: fadD5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O07411
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium formate, 20 % w/v SOKALAN CP 45

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→86.56 Å / Num. obs: 45898 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 79.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.053 / Rrim(I) all: 0.148 / Net I/σ(I): 10.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.8 % / Rmerge(I) obs: 2.32 / Num. unique obs: 4454 / CC1/2: 0.393 / Rpim(I) all: 0.868 / Rrim(I) all: 2.481 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→86.56 Å / SU ML: 0.495 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4374
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2384 2345 5.11 %
Rwork0.2052 43520 -
obs0.2069 45865 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.86 Å2
Refinement stepCycle: LAST / Resolution: 2.8→86.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6248 0 30 53 6331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196403
X-RAY DIFFRACTIONf_angle_d0.47748733
X-RAY DIFFRACTIONf_chiral_restr0.0421021
X-RAY DIFFRACTIONf_plane_restr0.00491135
X-RAY DIFFRACTIONf_dihedral_angle_d12.00312296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.860.52811390.52832502X-RAY DIFFRACTION99.85
2.86-2.920.45261400.41172524X-RAY DIFFRACTION99.92
2.92-2.990.39491280.35532547X-RAY DIFFRACTION99.93
2.99-3.060.39721290.30262517X-RAY DIFFRACTION99.96
3.06-3.140.281390.26612533X-RAY DIFFRACTION99.78
3.14-3.240.25211370.24372541X-RAY DIFFRACTION99.89
3.24-3.340.32551420.24552526X-RAY DIFFRACTION99.81
3.34-3.460.26381510.2542544X-RAY DIFFRACTION99.67
3.46-3.60.28541620.27282491X-RAY DIFFRACTION99.62
3.6-3.760.25661210.19332566X-RAY DIFFRACTION99.59
3.76-3.960.24811350.17282544X-RAY DIFFRACTION99.55
3.96-4.210.17821510.16062545X-RAY DIFFRACTION99.52
4.21-4.540.20491310.16612577X-RAY DIFFRACTION99.49
4.54-4.990.17231270.16392581X-RAY DIFFRACTION99.19
4.99-5.710.20051290.18012619X-RAY DIFFRACTION99.13
5.71-7.20.25391450.19942613X-RAY DIFFRACTION98.75
7.2-86.560.18221390.1722750X-RAY DIFFRACTION97.17
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)
13.97076777883-1.57062198025-0.2900262474254.94700614627-0.3120779979964.134553825890.0938054419585-0.165644658354-0.151956631236-0.0502338513757-0.255118896966-0.5646291402330.01434007191580.8167691178080.1316471110640.41564219411-0.0263144442321-0.07169313641460.5953848001410.09284385997590.675267357986-3.7856366970743.956366285736.9621053116
26.01911476423-1.439611909572.490126884873.22591404823-1.244722141897.58771724569-0.202681627348-0.116713236910.0951183197776-0.189508149509-0.175925739303-0.9574012945680.001856532138141.169001388760.2597343780250.5347458246220.0226489474214-0.02108062235040.6505911631840.1089611417120.793914675677-1.3082427688639.915642443333.8045239387
31.573513644730.7317249886290.402623165181.9255919605-0.05070265962662.60503286805-0.00552609856761-0.0521618676387-0.15566997183-0.0307149776193-0.01170492416930.06078725912420.205158457034-0.09719007820580.01740167779370.5620819378340.0156223005353-0.012441167310.3824332184450.05930549396250.521557000547-26.629969965734.46353530334.5475793744
42.474375420810.327030512187-0.3876727367595.80672362521-2.721426178855.28201622217-0.05595595232760.6142553351680.0458840559396-0.5646610922910.3633499941010.282453380260.388397935768-0.700960556742-0.315395830160.474553462278-0.0706191836138-0.05918709567430.605693366210.1007346664250.485338471114-35.91269858955.57708514520.0932244991459
55.646578121951.76552099735-2.076220364042.15871077761-1.886251459667.17808527857-0.0551504963252-0.0938362017087-0.11646866990.300838993632-0.00502701765153-0.0599569302091-0.0006535554304790.3214393441530.07842668122430.4231327537810.0167398717415-0.03606928494180.3426029490390.01074975527120.529516207289-28.499243733558.53032035916.0196481926
62.130142821820.6450163341960.8247277217552.41469779350.3113842597121.800021159040.022725714297-0.2135847119880.3029341051030.4699653370320.08265145005310.270605611045-0.285617477429-0.324581745511-0.09999541501280.6005031105190.05049176611560.1006891113920.4233910709260.08802878834270.549978047518-33.002942966166.51002827426.4382784736
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 36 through 127 )AA36 - 12717 - 108
22chain 'A' and (resid 128 through 215 )AA128 - 215109 - 196
33chain 'A' and (resid 216 through 451 )AA216 - 435197 - 416
44chain 'B' and (resid 36 through 179 )BB36 - 17917 - 160
55chain 'B' and (resid 180 through 234 )BB180 - 234161 - 215
66chain 'B' and (resid 235 through 452 )BB235 - 436216 - 417

+
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