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- PDB-7des: Acyl-Coenzyme A Binding Protein 103 (LMJF_17_0620) of Leishmania Major -

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Basic information

Entry
Database: PDB / ID: 7des
TitleAcyl-Coenzyme A Binding Protein 103 (LMJF_17_0620) of Leishmania Major
ComponentsACB domain-containing protein
KeywordsLIPID BINDING PROTEIN / Fatty-acyl-Coa-binding protein
Function / homology
Function and homology information


fatty-acyl-CoA binding / ciliary plasm / fatty acid metabolic process / nucleoplasm / cytoplasm
Similarity search - Function
Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / FERM/acyl-CoA-binding protein superfamily
Similarity search - Domain/homology
FORMIC ACID / ACB domain-containing protein
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsVerma, S. / Sundd, M. / Makde, R.D.
CitationJournal: To Be Published
Title: Acyl-Coenzyme A Binding Protein 103 (LMJF_17_0620) of Leishmania Major
Authors: Verma, S. / Sundd, M. / Makde, R.D.
History
DepositionNov 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACB domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6004
Polymers11,4621
Non-polymers1383
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint0 kcal/mol
Surface area5920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.946, 36.996, 58.611
Angle α, β, γ (deg.)90.000, 104.016, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein ACB domain-containing protein


Mass: 11462.015 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_17_0620 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q4QED2
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.01 % / Description: rod-shaped crystals
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 3350, 0.2M Magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryostream - 700 series / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 25, 2018
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.4→40.68 Å / Num. obs: 17287 / % possible obs: 99 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Net I/σ(I): 19.2
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 978 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IJM

5ijm


Resolution: 1.45→22.77 Å / SU ML: 0.1152 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.2643
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1935 921 5.33 %
Rwork0.1648 16366 -
obs0.1664 17287 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.04 Å2
Refinement stepCycle: LAST / Resolution: 1.45→22.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms741 0 9 88 838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052785
X-RAY DIFFRACTIONf_angle_d0.77081067
X-RAY DIFFRACTIONf_chiral_restr0.058115
X-RAY DIFFRACTIONf_plane_restr0.0036137
X-RAY DIFFRACTIONf_dihedral_angle_d16.4923285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.530.19911170.14842344X-RAY DIFFRACTION99.76
1.53-1.620.2161310.15062347X-RAY DIFFRACTION99.76
1.62-1.750.22891540.15542327X-RAY DIFFRACTION99.88
1.75-1.920.21041250.15642333X-RAY DIFFRACTION99.31
1.92-2.20.21431440.14442332X-RAY DIFFRACTION99.4
2.2-2.770.19981100.17152364X-RAY DIFFRACTION98.8
2.77-22.770.16991400.17682319X-RAY DIFFRACTION96.02

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