[English] 日本語
Yorodumi
- PDB-5ab5: Crystal structure of Trypanosoma brucei SCP2-thiolase like protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ab5
TitleCrystal structure of Trypanosoma brucei SCP2-thiolase like protein (TbSLP) form-II.
ComponentsSCP2-THIOLASE LIKE PROTEIN
KeywordsTRANSPORT PROTEIN / COENZYME A / SCP2-THIOLASE / SCP2-THIOLASE-LIKE PROTEIN / MALONYL-COA DECARBOXYLASE / GENE KNOCKOUT / LIPID METABOLISM
Function / homologyThiolase / acyltransferase activity, transferring groups other than amino-acyl groups / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta / Nonspecific lipid-transfer protein, putative
Function and homology information
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHarijan, R.K. / Kiema, T.R. / Wierenga, R.K.
CitationJournal: Proteins / Year: 2016
Title: The Scp2-Thiolase-Like Protein (Slp) of Trypanosoma Brucei is an Enzyme Involved in Lipid Metabolism.
Authors: Harijan, R.K. / Mazet, M. / Kiema, T.R. / Bouyssou, G. / Alexson, S.E.H. / Bergmann, U. / Moreau, P. / Michels, P.A.M. / Bringaud, F. / Wierenga, R.K.
History
DepositionAug 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: SCP2-THIOLASE LIKE PROTEIN
B: SCP2-THIOLASE LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,98115
Polymers90,7322
Non-polymers1,24913
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-193.1 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.689, 66.689, 157.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.4979, -0.8672, -0.002531), (-0.8672, 0.4979, -5.1E-5), (0.001304, 0.002169, -1)
Vector: 133.3, 77.18, 9.747)

-
Components

#1: Protein SCP2-THIOLASE LIKE PROTEIN


Mass: 45365.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: EATRO1125 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9ZUV7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.3 Å3/Da / Density % sol: 47.1 % / Description: NONE
Crystal growpH: 4.6
Details: 100 MM SODIUM ACETATE (PH 4.6), 2.0 M AMMONIUM SULPHATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2013
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twinOperator: H,-H-K,-L L / Fraction: 0.5
ReflectionResolution: 2→28.88 Å / Num. obs: 52628 / % possible obs: 99.8 % / Observed criterion σ(I): 1.3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.3 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.877 Å / σ(F): 1.96 / Phase error: 30.58 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2204 2554 4.9 %
Rwork0.1981 --
obs0.1996 52602 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6066 0 65 119 6250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036244
X-RAY DIFFRACTIONf_angle_d0.8928480
X-RAY DIFFRACTIONf_dihedral_angle_d12.8222248
X-RAY DIFFRACTIONf_chiral_restr0.057948
X-RAY DIFFRACTIONf_plane_restr0.0041108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0004-2.03880.39991570.35192767X-RAY DIFFRACTION94
2.0388-2.08040.32461390.32862796X-RAY DIFFRACTION94
2.0804-2.12560.35081330.30492706X-RAY DIFFRACTION94
2.1256-2.1750.28381520.30542794X-RAY DIFFRACTION94
2.175-2.22940.29731520.28962785X-RAY DIFFRACTION94
2.2294-2.28960.3741380.26952775X-RAY DIFFRACTION95
2.2896-2.35690.25271290.26982775X-RAY DIFFRACTION95
2.3569-2.43290.25661570.26482746X-RAY DIFFRACTION94
2.4329-2.51970.22331660.2732749X-RAY DIFFRACTION94
2.5197-2.62040.24691640.25772775X-RAY DIFFRACTION94
2.6204-2.73950.33181240.24142784X-RAY DIFFRACTION96
2.7395-2.88360.28361440.22972838X-RAY DIFFRACTION95
2.8836-3.06380.24821200.22632780X-RAY DIFFRACTION96
3.0638-3.29960.22231240.20032814X-RAY DIFFRACTION96
3.2996-3.63030.22871310.17272793X-RAY DIFFRACTION95
3.6303-4.15250.14771390.14372783X-RAY DIFFRACTION94
4.1525-5.21980.17111270.13352778X-RAY DIFFRACTION95
5.2198-21.83040.15571550.15482773X-RAY DIFFRACTION94

+
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://pdbjlvh1.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