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- PDB-5i87: Crystal structure of BT-CD domains of human acetyl-CoA carboxylase -

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Basic information

Entry
Database: PDB / ID: 5i87
TitleCrystal structure of BT-CD domains of human acetyl-CoA carboxylase
Components(BT-CD domains of human acetyl-CoA carboxylase) x 2
KeywordsLIGASE / Carboxylase / carrier protein-dependent enzyme / fatty acid metabolism / multienzyme
Function / homology:
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.7 Å
AuthorsStuttfeld, E. / Hunkeler, M. / Hagmann, A. / Imseng, S. / Maier, T.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation138262 Switzerland
Swiss National Science Foundation159696 Switzerland
Swiss National Science Foundation145023 Switzerland
CitationJournal: Nat Commun / Year: 2016
Title: The dynamic organization of fungal acetyl-CoA carboxylase.
Authors: Hunkeler, M. / Stuttfeld, E. / Hagmann, A. / Imseng, S. / Maier, T.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / database_2 / pdbx_entry_details
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: BT-CD domains of human acetyl-CoA carboxylase
B: BT-CD domains of human acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,4687
Polymers117,9062
Non-polymers5625
Water00
1
A: BT-CD domains of human acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7743
Polymers61,5491
Non-polymers2252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BT-CD domains of human acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6954
Polymers56,3581
Non-polymers3373
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)267.270, 267.270, 210.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein BT-CD domains of human acetyl-CoA carboxylase


Mass: 61548.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 1. Due to the low resolution of the diffraction data, authors could not identify the correct numbering/type of the residues. The residue numbering is arbitrary. The one-letter sequence for ...Details: 1. Due to the low resolution of the diffraction data, authors could not identify the correct numbering/type of the residues. The residue numbering is arbitrary. The one-letter sequence for the protein corresponds to Uniprot accession Q13085 residues 622-1584. 2. Residues 753-818 of Uniprot accession Q13085 were replaced by a GSG linker in the crystallized construct.
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: acetyl-CoA carboxylase
#2: Protein BT-CD domains of human acetyl-CoA carboxylase


Mass: 56357.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 1. Due to the low resolution of the diffraction data, authors could not identify the correct numbering/type of the residues. The residue numbering is arbitrary. The one-letter sequence for ...Details: 1. Due to the low resolution of the diffraction data, authors could not identify the correct numbering/type of the residues. The residue numbering is arbitrary. The one-letter sequence for the protein corresponds to Uniprot accession Q13085 residues 622-1584. 2. Residues 753-818 of Uniprot accession Q13085 were replaced by a GSG linker in the crystallized construct.
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: acetyl-CoA carboxylase
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
Has protein modificationN

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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

Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: MES, tri-potassium citrate, PEG10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→84.518 Å / Num. obs: 77629 / % possible obs: 99.8 % / Redundancy: 13.7 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.24
Reflection shellResolution: 3.7→3.8 Å / Redundancy: 13.7 % / Rmerge(I) obs: 4.01 / Mean I/σ(I) obs: 1.07 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSVERSION March 1, 2015data reduction
XSCALEVERSION March 1, 2015data scaling
SHELXCD2014/2phasing
RefinementMethod to determine structure: SAD / Resolution: 3.7→84.518 Å / SU ML: 0.91 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 51.48
RfactorNum. reflection% reflection
Rfree0.3807 2036 5.01 %
Rwork0.3468 --
obs0.3485 40647 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.7→84.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6925 0 5 0 6930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046882
X-RAY DIFFRACTIONf_angle_d0.8329566
X-RAY DIFFRACTIONf_dihedral_angle_d4.7091342
X-RAY DIFFRACTIONf_chiral_restr0.0281385
X-RAY DIFFRACTIONf_plane_restr0.0031342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7003-3.78640.57511350.49822528X-RAY DIFFRACTION99
3.7864-3.8810.50641370.45782537X-RAY DIFFRACTION99
3.881-3.9860.42681310.45632518X-RAY DIFFRACTION99
3.986-4.10330.51521300.44862542X-RAY DIFFRACTION100
4.1033-4.23570.49031280.42532564X-RAY DIFFRACTION100
4.2357-4.38710.44471200.39412551X-RAY DIFFRACTION100
4.3871-4.56270.44951460.38082535X-RAY DIFFRACTION100
4.5627-4.77040.41361160.38152567X-RAY DIFFRACTION100
4.7704-5.02180.42211450.37372565X-RAY DIFFRACTION100
5.0218-5.33640.4591420.38582564X-RAY DIFFRACTION100
5.3364-5.74840.39341260.42122578X-RAY DIFFRACTION100
5.7484-6.32670.53891320.40542602X-RAY DIFFRACTION100
6.3267-7.24170.39631570.36592592X-RAY DIFFRACTION100
7.2417-9.12210.30711380.27092630X-RAY DIFFRACTION100
9.1221-84.54020.31151530.2952738X-RAY DIFFRACTION99

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