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- PDB-5zwt: Crystal structure of the S37A mutant of apo-acyl carrier protein ... -

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Basic information

Entry
Database: PDB / ID: 5zwt
TitleCrystal structure of the S37A mutant 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSharma, B. / Arya, R. / Kundu, S. / Makde, R.D.
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
A: Acyl carrier protein
B: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)18,5432
Polymers18,5432
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint2 kcal/mol
Surface area9030 Å2
Unit cell
Length a, b, c (Å)83.506, 83.506, 99.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-113-

HOH

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Components

#1: Protein Acyl carrier protein /


Mass: 9271.485 Da / Num. of mol.: 2 / Mutation: S107A
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.: 72 / 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: 47.45 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 7.5 / Details: 0.1M HEPES, pH 7.5, 2.0M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→41.75 Å / Num. obs: 11845 / % possible obs: 96.7 % / Redundancy: 10.6 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.021 / Net I/σ(I): 21.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.956 / Num. unique obs: 886 / CC1/2: 0.819 / Rpim(I) all: 0.303 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X3O

1x3o


Resolution: 2→31.993 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4
RfactorNum. reflection% reflection
Rfree0.2721 578 4.97 %
Rwork0.2343 --
obs0.2362 11637 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→31.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 0 72 1321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071267
X-RAY DIFFRACTIONf_angle_d0.8771728
X-RAY DIFFRACTIONf_dihedral_angle_d18.227770
X-RAY DIFFRACTIONf_chiral_restr0.059214
X-RAY DIFFRACTIONf_plane_restr0.009227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20120.26561520.2832855X-RAY DIFFRACTION100
2.2012-2.51960.32541200.29652420X-RAY DIFFRACTION84
2.5196-3.1740.30011570.26092880X-RAY DIFFRACTION100
3.174-31.99740.24981490.20272904X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -24.7773 Å / Origin y: -2.0873 Å / Origin z: -25.8077 Å
111213212223313233
T0.2616 Å20.0551 Å20.0273 Å2-0.2709 Å20.0323 Å2--0.2368 Å2
L0.6322 °2-0.1367 °20.5033 °2-1.7695 °2-1.3833 °2--1.5539 °2
S0.1236 Å °-0.1018 Å °-0.0218 Å °-0.2599 Å °-0.0249 Å °0.1912 Å °0.1032 Å °0.6184 Å °0.2689 Å °
Refinement TLS groupSelection details: all

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