[English] 日本語
Yorodumi
- PDB-5lnq: Crystal structure of SCP2 thiolase from Leishmania mexicana. Comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lnq
TitleCrystal structure of SCP2 thiolase from Leishmania mexicana. Complex of the C123A mutant with acetoacetyl-CoA.
Components3-ketoacyl-CoA thiolase-like protein
KeywordsTRANSFERASE / Leishmania mexicana / SCP2-thiolase / acetoacetyl-coA / lipid metabolism
Function / homology
Function and homology information


propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / lipid transport / lipid binding
Similarity search - Function
Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like ...Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETOACETYL-COENZYME A / propanoyl-CoA C-acyltransferase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHarijan, R.K. / Kiema, T.-R. / Wierenga, R.K.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland131795 Finland
BioStruct-X283570 Finland
European Commissions Seventh Framework ProgrammeFP7/2007-2013 Finland
CitationJournal: Protein Eng. Des. Sel. / Year: 2017
Title: Crystallographic substrate binding studies of Leishmania mexicana SCP2-thiolase (type-2): unique features of oxyanion hole-1.
Authors: Harijan, R.K. / Kiema, T.R. / Syed, S.M. / Qadir, I. / Mazet, M. / Bringaud, F. / Michels, P.A.M. / Wierenga, R.K.
History
DepositionAug 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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_ncs_dom_lim
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-ketoacyl-CoA thiolase-like protein
B: 3-ketoacyl-CoA thiolase-like protein
C: 3-ketoacyl-CoA thiolase-like protein
D: 3-ketoacyl-CoA thiolase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,4597
Polymers196,9044
Non-polymers2,5553
Water14,952830
1
A: 3-ketoacyl-CoA thiolase-like protein
B: 3-ketoacyl-CoA thiolase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1554
Polymers98,4522
Non-polymers1,7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-22 kcal/mol
Surface area28080 Å2
MethodPISA
2
C: 3-ketoacyl-CoA thiolase-like protein
D: 3-ketoacyl-CoA thiolase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3033
Polymers98,4522
Non-polymers8521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-21 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.141, 89.804, 123.716
Angle α, β, γ (deg.)90.00, 104.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 12 - 441 / Label seq-ID: 28 - 457

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
3-ketoacyl-CoA thiolase-like protein


Mass: 49225.926 Da / Num. of mol.: 4 / Mutation: C123A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Gene: LMXM_23_0690 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9AW84, acetyl-CoA C-acyltransferase
#2: Chemical ChemComp-CAA / ACETOACETYL-COENZYME A / Acetoacetyl-CoA


Mass: 851.607 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 830 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Bis Tris propane, pH 7.5, 0.2M sodium fluoride and 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 31, 2014
RadiationMonochromator: silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.98→119.63 Å / Num. obs: 108328 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.9
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / CC1/2: 0.57 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZBN

3zbn


Resolution: 1.98→119.63 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.012 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.168 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22607 5300 4.9 %RANDOM
Rwork0.18934 ---
obs0.19113 103007 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.087 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å2-0 Å20.34 Å2
2---1.46 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.98→119.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12892 0 162 830 13884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01913412
X-RAY DIFFRACTIONr_bond_other_d0.010.0212774
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.98618127
X-RAY DIFFRACTIONr_angle_other_deg1.652329431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44751724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93924.786560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.585152276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9731568
X-RAY DIFFRACTIONr_chiral_restr0.120.22002
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215355
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022962
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1452.1736884
X-RAY DIFFRACTIONr_mcbond_other2.1442.1736883
X-RAY DIFFRACTIONr_mcangle_it3.3583.2518600
X-RAY DIFFRACTIONr_mcangle_other3.3583.2518601
X-RAY DIFFRACTIONr_scbond_it3.212.8046528
X-RAY DIFFRACTIONr_scbond_other3.212.8066529
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.114.0549524
X-RAY DIFFRACTIONr_long_range_B_refined7.09118.55115170
X-RAY DIFFRACTIONr_long_range_B_other7.0918.55915171
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A523620.08
12B523620.08
21A528220.07
22C528220.07
31A527100.07
32D527100.07
41B523880.08
42C523880.08
51B528680.08
52D528680.08
61C521740.08
62D521740.08
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 409 -
Rwork0.255 7561 -
obs--99.14 %

+
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