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- PDB-5i6i: Crystal structure of a dBCCP-variant of Chaetomium thermophilum a... -

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Basic information

Entry
Database: PDB / ID: 5i6i
TitleCrystal structure of a dBCCP-variant of Chaetomium thermophilum acetyl-CoA carboxylase
ComponentsAcetyl-CoA carboxylase-like protein,Acetyl-CoA carboxylase-like protein,Acetyl-CoA carboxylase-like protein
KeywordsLIGASE / Carboxylase / Fatty acid metabolism / Multienzyme / Carrier protein-dependent enzyme
Function / homology
Function and homology information


biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase ...Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Rudiment single hybrid motif / Single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Acetyl-CoA carboxylase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 8.4 Å
AuthorsHunkeler, M. / Stuttfeld, E. / 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 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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
A: Acetyl-CoA carboxylase-like protein,Acetyl-CoA carboxylase-like protein,Acetyl-CoA carboxylase-like protein
B: Acetyl-CoA carboxylase-like protein,Acetyl-CoA carboxylase-like protein,Acetyl-CoA carboxylase-like protein


Theoretical massNumber of molelcules
Total (without water)497,4812
Polymers497,4812
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13400 Å2
ΔGint-105 kcal/mol
Surface area129670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)462.200, 462.200, 204.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Acetyl-CoA carboxylase-like protein,Acetyl-CoA carboxylase-like protein,Acetyl-CoA carboxylase-like protein


Mass: 248740.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The crystallized construct contains amino acids 1-2297 (aligned to accession code: G0S3L5). The carrier protein (residues 701-766 aligned to accession code G0S3L5) was removed from the ...Details: The crystallized construct contains amino acids 1-2297 (aligned to accession code: G0S3L5). The carrier protein (residues 701-766 aligned to accession code G0S3L5) was removed from the construct and replaced by a GSG linker. Due to formatting restrictions the SEQRES card was truncated C-terminally to residue R2261. C-terminal stretches after L2259 in chain A could not be modeled unambiguously and were interpreted as poly-Ala/UNK residues
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus), (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0021690 / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0S3L5, acetyl-CoA carboxylase

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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: 6.34 Å3/Da / Density % sol: 80.61 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop
Details: Morpheus buffer system 3, Morpheus ethylene glycol mix, PEG4000, Glycerol
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99986 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 8.4→49.95 Å / Num. obs: 12113 / % possible obs: 99.1 % / Redundancy: 18.5 % / Biso Wilson estimate: 751.38 Å2 / Rmerge(I) obs: 0.294 / Net I/σ(I): 9.05
Reflection shellResolution: 8.4→8.62 Å / Redundancy: 18.2 % / Rmerge(I) obs: 3.82 / Mean I/σ(I) obs: 0.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSVERSION March 1, 2015data reduction
XSCALEVERSION March 1, 2015data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i6f, 5i6e

5i6f

5i6e


Resolution: 8.4→49.95 Å / Cor.coef. Fo:Fc: 0.6999 / Cor.coef. Fo:Fc free: 0.6775 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 3.654
RfactorNum. reflection% reflectionSelection details
Rfree0.3236 549 4.53 %RANDOM
Rwork0.2968 ---
obs0.2981 12111 99.7 %-
Displacement parametersBiso mean: 250.2 Å2
Baniso -1Baniso -2Baniso -3
1-112.2897 Å20 Å20 Å2
2--112.2897 Å20 Å2
3----224.5795 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: LAST / Resolution: 8.4→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22445 0 0 0 22445
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00822918HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0131027HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10772SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes618HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3293HARMONIC5
X-RAY DIFFRACTIONt_it22918HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion3.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2911SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact25953SEMIHARMONIC4
LS refinement shellResolution: 8.4→9.2 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3138 118 4.15 %
Rwork0.2542 2725 -
all0.2564 2843 -
obs--99.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
117.38484.3656-11.927132.50783.195924.94630.4223-0.09381.0546-0.2688-0.8273-0.63331.35190.92390.4051.3068-0.2280.09640.517-0.47090.9119-36.250715.083853.2108
211.148315.16771.065313.7983.975724.94630.5916-1.22911.7980.57240.06850.1512-2.16790.4894-0.66010.5876-0.3392-0.12420.62830.45480.304-59.542655.064274.7779
3-7.21413.76391.84618.6036-9.01618.7890.06711.247-0.1077-0.28440.8788-1.00680.54671.9297-0.9459-1.04350.0760.6228-0.7803-0.1669-0.9119-69.982654.929148.1248
41.05821.1636-0.15446.2209-5.29263.79060.4814-0.28960.7435-0.58050.0628-0.1992-1.1419-1.2877-0.5442-0.517-0.2280.4709-1.30680.0964-0.9119-106.877588.401925.0697
532.5078-4.3656-6.886117.38486.106324.9463-1.49040.45750.2032-0.11541.4212-0.6566-1.57980.94880.06920.79070.24550.16250.42520.62030.9119-85.8338191.8525-6.7313
69.6448-12.7698-1.845115.30159.016724.0820.38342.1452-2.0903-1.1202-0.20830.3552.1024-0.4844-0.17510.80830.23530.60480.4075-0.13560.3593-113.257153.3344-24.2335
716.6457-3.2982-3.195922.8201-11.927101.045-0.54260.3307-0.4466-1.6865-0.2315-1.29031.14030.6415-0.517-0.2280.1669-1.30680.6228-0.1869-106.6313152.72343.8376
82.7431-1.60061.63765.0952-1.68464.0050.4025-0.58652.23041.03370.5404-0.5976-1.1419-1.2877-0.9429-0.517-0.2280.6228-1.3068-0.1669-0.9119-109.5375109.990137.9253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|788 - 1031}
2X-RAY DIFFRACTION2{A|1040 - 1327}
3X-RAY DIFFRACTION3{A|1328 - 1523}
4X-RAY DIFFRACTION4{A|1524 - 2259}
5X-RAY DIFFRACTION5{B|788 - 1032}
6X-RAY DIFFRACTION6{B|1036 - 1327}
7X-RAY DIFFRACTION7{B|1328 - 1523}
8X-RAY DIFFRACTION8{B|1524 - 2259}

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