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- PDB-6kf8: OsACBP2 in complex with C18:3-CoA -

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Basic information

Entry
Database: PDB / ID: 6kf8
TitleOsACBP2 in complex with C18:3-CoA
ComponentsAcyl-CoA-binding domain-containing protein 2
KeywordsPLANT PROTEIN / Plant / transporter / CoA / Fatty acyl
Function / homologyAcyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / fatty-acyl-CoA binding / FERM/acyl-CoA-binding protein superfamily / fatty acid metabolic process / cytosol / Acyl-CoA-binding domain-containing protein 2
Function and homology information
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsJin, J. / Chye, M.L.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: To Be Published
Title: OsACBP2 in complex with C18:3-CoA
Authors: Jin, J. / Chye, M.L.
History
DepositionJul 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: 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

Downloads & links

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Assembly

Deposited unit
C: Acyl-CoA-binding domain-containing protein 2
A: Acyl-CoA-binding domain-containing protein 2
D: Acyl-CoA-binding domain-containing protein 2
F: Acyl-CoA-binding domain-containing protein 2
I: Acyl-CoA-binding domain-containing protein 2
K: Acyl-CoA-binding domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)62,4346
Polymers62,4346
Non-polymers00
Water00
1
C: Acyl-CoA-binding domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)10,4061
Polymers10,4061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Acyl-CoA-binding domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)10,4061
Polymers10,4061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Acyl-CoA-binding domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)10,4061
Polymers10,4061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Acyl-CoA-binding domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)10,4061
Polymers10,4061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Acyl-CoA-binding domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)10,4061
Polymers10,4061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Acyl-CoA-binding domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)10,4061
Polymers10,4061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.965, 149.965, 95.443
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Acyl-CoA-binding domain-containing protein 2 / OsACBP2


Mass: 10405.707 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: ACBP2, Os06g0115300, LOC_Os06g02490, OsJ_19900, OSJNBa0019F11.14, P0541H01.36
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q5VRM0
Has ligand of interestN

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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: 3.4 Å3/Da / Density % sol: 63.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97894 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 3.51→79.91 Å / Num. obs: 9948 / % possible obs: 99.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 6.8
Reflection shellResolution: 3.51→3.7 Å / Rmerge(I) obs: 0.522 / Num. unique obs: 1445

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H3I

5h3i


Resolution: 3.6→44.83 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.837 / SU B: 33.584 / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.703 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2792 323 3.5 %RANDOM
Rwork0.2281 ---
obs0.2299 8924 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 257.57 Å2 / Biso mean: 87.201 Å2 / Biso min: 43.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 3.6→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4241 0 0 0 4241
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134339
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174099
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.6545853
X-RAY DIFFRACTIONr_angle_other_deg1.2381.5899587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28525204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.98515821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.9591512
X-RAY DIFFRACTIONr_chiral_restr0.0570.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024763
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02833
LS refinement shellResolution: 3.601→3.694 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 18 -
Rwork0.218 667 -
all-685 -
obs--97.72 %

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