[English] 日本語
Yorodumi
- PDB-2op0: Crystal structure of plasmodium falciparum enoyl ACP reductase wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2op0
TitleCrystal structure of plasmodium falciparum enoyl ACP reductase with triclosan reductase
ComponentsEnoyl-acyl carrier reductase
KeywordsOXIDOREDUCTASE / PfENR / malaria / triclosan analog
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 / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7PC / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-ACP reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTsai, H.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: X-ray structural analysis of Plasmodium falciparum enoyl acyl carrier protein reductase as a pathway toward the optimization of triclosan antimalarial efficacy
Authors: Freundlich, J.S. / Wang, F. / Tsai, H.-C. / Kuo, M. / Shieh, H.-M. / Anderson, J.W. / Nkrumah, L.J. / Valderramos, J.-C. / Yu, M. / Kumar, T.R.S. / Valderramos, S.G. / Jacobs, W.R. / ...Authors: Freundlich, J.S. / Wang, F. / Tsai, H.-C. / Kuo, M. / Shieh, H.-M. / Anderson, J.W. / Nkrumah, L.J. / Valderramos, J.-C. / Yu, M. / Kumar, T.R.S. / Valderramos, S.G. / Jacobs, W.R. / Schiehser, G.A. / Jacobus, D.P. / Fidock, D.A. / Sacchettini, J.C.
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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-acyl carrier reductase
B: Enoyl-acyl carrier reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7855
Polymers76,6992
Non-polymers1,0863
Water1,964109
1
A: Enoyl-acyl carrier reductase
B: Enoyl-acyl carrier reductase
hetero molecules

A: Enoyl-acyl carrier reductase
B: Enoyl-acyl carrier reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,57010
Polymers153,3974
Non-polymers2,1736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area20860 Å2
ΔGint-161 kcal/mol
Surface area38530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.305, 132.305, 82.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Enoyl-acyl carrier reductase / Enoyl-ACP reductase


Mass: 38349.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: FabI / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon+-RIL cells
References: UniProt: Q9BH77, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-7PC / 2-[4-(AMINOMETHYL)-2-CHLOROPHENOXY]-5-PYRIDIN-2-YLPHENOL


Mass: 326.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15ClN2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.35M (NH4)2SO4, 0.1M AcONa, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 18748 / Num. obs: 18311 / % possible obs: 97.67 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Net I/σ(I): 21.69
Reflection shellResolution: 2.8→2.9 Å / % possible all: 99.68

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NHD

1nhd
PDB Unreleased entry


Resolution: 2.8→93.66 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.873 / SU B: 14.601 / SU ML: 0.297 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27371 931 5.1 %RANDOM
Rwork0.18689 ---
obs0.19122 17379 97.9 %-
all-18311 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.405 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.8→93.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4416 0 72 109 4597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0410.0224573
X-RAY DIFFRACTIONr_angle_refined_deg3.2611.9826175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6345553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.34924.747198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.27215820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6311519
X-RAY DIFFRACTIONr_chiral_restr0.2110.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.023372
X-RAY DIFFRACTIONr_nbd_refined0.2920.22305
X-RAY DIFFRACTIONr_nbtor_refined0.3550.23149
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.2131
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4010.221
X-RAY DIFFRACTIONr_mcbond_it1.8041.52895
X-RAY DIFFRACTIONr_mcangle_it2.79224459
X-RAY DIFFRACTIONr_scbond_it4.26932035
X-RAY DIFFRACTIONr_scangle_it6.1144.51716
LS refinement shellResolution: 2.798→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 69 -
Rwork0.27 1280 -
obs--99.85 %

+
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