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- PDB-5zws: Crystal structure of apo-acyl carrier protein from Leishmania major -

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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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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