[English] 日本語
Yorodumi
- PDB-2o2s: The structure of T. gondii enoyl acyl carrier protein reductase i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o2s
TitleThe structure of T. gondii enoyl acyl carrier protein reductase in complex with NAD and triclosan
ComponentsEnoyl-acyl carrier reductase
KeywordsOXIDOREDUCTASE / enoyl reductase / triclosan / Rossmann fold
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRICLOSAN / Enoyl-acyl carrier reductase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMuench, S.P. / Prigge, S.T. / McLeod, R. / Rafferty, J.B. / Kirisits, M.J. / Roberts, C.W. / Mui, E.J. / Rice, D.W.
Citation
Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007
Title: Studies of Toxoplasma gondii and Plasmodium falciparum enoyl acyl carrier protein reductase and implications for the development of antiparasitic agents
Authors: Muench, S.P. / Prigge, S.T. / McLeod, R. / Rafferty, J.B. / Kirisits, M.J. / Roberts, C.W. / Mui, E.J. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Expression, purification and preliminary crystallographic analysis of the Toxoplasma gondii enoyl reductase
Authors: Muench, S.P. / Prigge, S.T. / Zhu, L. / Kirisits, M.J. / Roberts, C.W. / Wernimont, S. / McLeod, R. / Rice, D.W.
History
DepositionNov 30, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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)68,6896
Polymers66,7832
Non-polymers1,9064
Water64936
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)137,37812
Polymers133,5664
Non-polymers3,8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area24600 Å2
ΔGint-215 kcal/mol
Surface area40180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.075, 78.075, 187.955
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROPROAA4 - 3054 - 305
2PHEPHEBB3 - 3053 - 305

-
Components

#1: Protein Enoyl-acyl carrier reductase


Mass: 33391.555 Da / Num. of mol.: 2 / Fragment: residues 103-417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: ENR / Plasmid: pMALc2x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3)
References: UniProt: Q6UCJ9, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-TCL / TRICLOSAN / Triclosan


Mass: 289.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Comment: antifungal, antibiotic, detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.48 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tris-HCL, 6% PEG 8000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2004 / Details: mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 21105 / Num. obs: 21105 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.082
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5 % / Rmerge(I) obs: 0.48 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O2Y

2o2y


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 13.006 / SU ML: 0.264 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.049 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26692 1080 5.1 %RANDOM
Rwork0.20492 ---
obs0.208 19990 99.73 %-
all-21105 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.158 Å2
Baniso -1Baniso -2Baniso -3
1-3.86 Å21.93 Å20 Å2
2--3.86 Å20 Å2
3----5.79 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 122 36 4672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224753
X-RAY DIFFRACTIONr_bond_other_d0.0010.024271
X-RAY DIFFRACTIONr_angle_refined_deg1.6212.0016468
X-RAY DIFFRACTIONr_angle_other_deg0.9539918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0655605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2323.743187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3815722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0351528
X-RAY DIFFRACTIONr_chiral_restr0.1050.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02963
X-RAY DIFFRACTIONr_nbd_refined0.2230.21046
X-RAY DIFFRACTIONr_nbd_other0.1830.24343
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22298
X-RAY DIFFRACTIONr_nbtor_other0.0880.22834
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.2140
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.225
X-RAY DIFFRACTIONr_mcbond_it0.5731.53054
X-RAY DIFFRACTIONr_mcbond_other0.1191.51250
X-RAY DIFFRACTIONr_mcangle_it0.9924763
X-RAY DIFFRACTIONr_scbond_it1.33131946
X-RAY DIFFRACTIONr_scangle_it2.1344.51705
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1765medium positional0.20.5
2577loose positional0.565
1765medium thermal0.692
2577loose thermal1.2610
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 87 -
Rwork0.31 1401 -
obs--99.8 %

+
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