[English] 日本語
Yorodumi
- PDB-3lt1: Enoyl-ACP Reductase from Plasmodium falciparum (PfENR) in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lt1
TitleEnoyl-ACP Reductase from Plasmodium falciparum (PfENR) in complex with triclosan variant T2
ComponentsEnoyl-ACP reductase
KeywordsOXIDOREDUCTASE / Triclosan / Triclosan variant / Enoyl-ACP reductase / P.falciparum
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-(chloromethyl)-2-(2,4-dichlorophenoxy)phenol / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-ACP reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMaity, K. / Bhargav, S.P. / Sankaran, B. / Surolia, N. / Surolia, A. / Suguna, K.
CitationJournal: Iubmb Life / Year: 2010
Title: X-ray crystallographic analysis of the complexes of enoyl acyl carrier protein reductase of Plasmodium falciparum with triclosan variants to elucidate the importance of different functional ...Title: X-ray crystallographic analysis of the complexes of enoyl acyl carrier protein reductase of Plasmodium falciparum with triclosan variants to elucidate the importance of different functional groups in enzyme inhibition
Authors: Maity, K. / Bhargav, S.P. / Sankaran, B. / Surolia, N. / Surolia, A. / Suguna, K.
History
DepositionFeb 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enoyl-ACP reductase
B: Enoyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4226
Polymers74,4882
Non-polymers1,9344
Water6,882382
1
A: Enoyl-ACP reductase
B: Enoyl-ACP reductase
hetero molecules

A: Enoyl-ACP reductase
B: Enoyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,84512
Polymers148,9774
Non-polymers3,8688
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area16570 Å2
ΔGint-97 kcal/mol
Surface area39350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.107, 131.107, 82.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Enoyl-ACP reductase


Mass: 37244.184 Da / Num. of mol.: 2 / Fragment: residues 96-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: fabI / Plasmid: PET-28a(+)(NOVAGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BJJ9, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-FT2 / 5-(chloromethyl)-2-(2,4-dichlorophenoxy)phenol


Mass: 303.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9Cl3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.8-3M ammonium sulphate, 0.1M MES buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 20, 2008 / Details: Vertically focusing RhPt coated mirror
RadiationMonochromator: Horizontally focussing asymmetric-cut single bounce Si(220) bent crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.2→47.9 Å / Num. obs: 37309 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 24.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3656 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UH5

1uh5


Resolution: 2.2→47.89 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.388 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.22455 1859 5 %RANDOM
Rwork0.17954 ---
obs0.18177 35382 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.809 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4404 0 124 382 4910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224676
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9926355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2545587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20124.526190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34615769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1471519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213489
X-RAY DIFFRACTIONr_mcbond_it1.0061.52880
X-RAY DIFFRACTIONr_mcangle_it1.85824606
X-RAY DIFFRACTIONr_scbond_it2.64531796
X-RAY DIFFRACTIONr_scangle_it4.2234.51744
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 121 -
Rwork0.27 2576 -
obs--99.56 %

+
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