[English] 日本語
Yorodumi
- PDB-5zws: Crystal structure of apo-acyl carrier protein from Leishmania major -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zws
TitleCrystal structure of apo-acyl carrier protein from Leishmania major
ComponentsAcyl carrier protein
KeywordsLIPID BINDING PROTEIN / Leishmania major / Acyl carrier protein / Fatty acid biosynthesis
Function / homology
Function and homology information


acyl binding / acyl carrier activity / mitochondrial respiratory chain complex I / fatty acid biosynthetic process / mitochondrial matrix / mitochondrion
Similarity search - Function
Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Acyl carrier protein
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsArya, R. / Sharma, B. / Makde, R.D. / Kundu, S.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2018
Title: A conformational switch from a closed apo- to an open holo-form equips the acyl carrier protein for acyl chain accommodation.
Authors: Arya, R. / Sharma, B. / Dhembla, C. / Pal, R.K. / Patel, A.K. / Sundd, M. / Ghosh, B. / Makde, R.D. / Kundu, S.
History
DepositionMay 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Acyl carrier protein
A: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)18,5752
Polymers18,5752
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint3 kcal/mol
Surface area9750 Å2
Unit cell
Length a, b, c (Å)30.069, 47.442, 61.128
Angle α, β, γ (deg.)90.00, 92.81, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Acyl carrier protein /


Mass: 9287.485 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: ACP, LMJF_27_0290 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9AD06
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 0.2M sodium chloride, 25% w/v polyethelene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→47.44 Å / Num. obs: 11636 / % possible obs: 99 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.079 / Rrim(I) all: 0.185 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.526 / CC1/2: 0.765 / Rpim(I) all: 0.257

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X3O

1x3o


Resolution: 2→37.462 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.45
RfactorNum. reflection% reflection
Rfree0.2722 645 5.55 %
Rwork0.2521 --
obs0.2529 11623 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→37.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 0 10 1310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031322
X-RAY DIFFRACTIONf_angle_d0.5411795
X-RAY DIFFRACTIONf_dihedral_angle_d15.32813
X-RAY DIFFRACTIONf_chiral_restr0.043214
X-RAY DIFFRACTIONf_plane_restr0.005235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0005-2.20050.26531620.25832637X-RAY DIFFRACTION92
2.2005-2.5160.27721690.25712705X-RAY DIFFRACTION93
2.516-3.1590.30831240.26352788X-RAY DIFFRACTION96
3.159-11.51080.25521710.23762795X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -25.9652 Å / Origin y: -5.1154 Å / Origin z: -14.3582 Å
111213212223313233
T0.0055 Å20.0042 Å20.0003 Å2-0.004 Å20.0015 Å2--0.004 Å2
L0.002 °20.0011 °20.0002 °2-0.0013 °20.0002 °2--0.0034 °2
S0 Å °0.0005 Å °0.0009 Å °-0.0011 Å °-0.0005 Å °0.0004 Å °-0.0019 Å °-0.0014 Å °-0.0012 Å °
Refinement TLS groupSelection details: all

+
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