[English] 日本語
Yorodumi
- PDB-3ce7: Crystal structure of toxoplasma specific mitochondrial acyl carri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ce7
TitleCrystal structure of toxoplasma specific mitochondrial acyl carrier protein, 59.m03510
ComponentsSpecific mitochondrial acyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / malaria / toxo / Toxoplasma / mitochondrial / ACP / Fatty acid biosynthesis / Lipid synthesis / Phosphopantetheine / Structural Genomics / Structural Genomics Consortium / SGC
Function / homologyAcyl-carrier / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha / Specific mitochodrial acyl carrier protein
Function and homology information
Biological speciesToxoplasma (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsWernimont, A.K. / Dong, A. / Yang, C. / Khuu, C. / Lam, A. / Brand, V. / Kozieradzki, I. / Cossar, D. / Arrowsmith, C.H. / Bountra, C. ...Wernimont, A.K. / Dong, A. / Yang, C. / Khuu, C. / Lam, A. / Brand, V. / Kozieradzki, I. / Cossar, D. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Weigelt, J. / Bochkarev, A. / Hui, R. / Qiu, W. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of toxoplasma specific mitochondrial acyl carrier protein, 59.m03510.
Authors: Wernimont, A.K. / Dong, A. / Yang, C. / Khuu, C. / Lin, Y.H. / Lam, A. / Brand, V. / Kozieradzki, I. / Cossar, D. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Weigelt, J. / Bochkarev, ...Authors: Wernimont, A.K. / Dong, A. / Yang, C. / Khuu, C. / Lin, Y.H. / Lam, A. / Brand, V. / Kozieradzki, I. / Cossar, D. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Weigelt, J. / Bochkarev, A. / Hui, R. / Qiu, W.
History
DepositionFeb 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: 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 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Specific mitochondrial acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)12,1601
Polymers12,1601
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.696, 64.696, 38.139
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Specific mitochondrial acyl carrier protein


Mass: 12159.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma (eukaryote) / Genus: Toxoplasma / Gene: synthetic codon DNA / Plasmid: p15-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: D0VWT5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 35.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.5 M NH4SO4, 0.2 M K,Na Tartrate, 0.1 M Na Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. all: 11276 / Num. obs: 11276 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.056 / Χ2: 1.973 / Net I/σ(I): 21.5
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 6.18 / Num. unique all: 1054 / Rsym value: 0.183 / Χ2: 0.827 / % possible all: 93.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å24.67 Å
Translation2.5 Å24.67 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L0I

1l0i


Resolution: 1.64→32.34 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.502 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.103 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 539 4.8 %RANDOM
Rwork0.185 ---
all0.187 11265 --
obs0.187 11265 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.535 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å2-0.41 Å20 Å2
2---0.81 Å20 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.64→32.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms741 0 0 82 823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022756
X-RAY DIFFRACTIONr_angle_refined_deg1.0721.9581037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3875101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58726.42942
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16115134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.733154
X-RAY DIFFRACTIONr_chiral_restr0.0740.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02585
X-RAY DIFFRACTIONr_nbd_refined0.2080.2325
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2538
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.218
X-RAY DIFFRACTIONr_mcbond_it0.6711.5479
X-RAY DIFFRACTIONr_mcangle_it1.1952768
X-RAY DIFFRACTIONr_scbond_it1.923305
X-RAY DIFFRACTIONr_scangle_it3.064.5263
LS refinement shellResolution: 1.64→1.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 35 -
Rwork0.258 686 -
all-721 -
obs-1054 87.93 %

+
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