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- PDB-5i6g: Crystal structure of C-terminal variant 2 of Chaetomium thermophi... -

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Basic information

Entry
Database: PDB / ID: 5i6g
TitleCrystal structure of C-terminal variant 2 of Chaetomium thermophilum acetyl-CoA carboxylase
ComponentsAcetyl-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 / mitochondrion / 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, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-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, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-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 / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / 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: 4.5 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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details

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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
B: Acetyl-CoA carboxylase-like protein,Acetyl-CoA carboxylase-like protein


Theoretical massNumber of molelcules
Total (without water)263,8132
Polymers263,8132
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13300 Å2
ΔGint-99 kcal/mol
Surface area90890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.170, 153.450, 249.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 131906.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The crystallized construct contains amino acids 1114-2297 (aligned to accession code: G0S3L5). Due to formatting restrictions the SEQRES card was truncated C-terminally to residue R2261. C- ...Details: The crystallized construct contains amino acids 1114-2297 (aligned to accession code: G0S3L5). Due to formatting restrictions the SEQRES card was truncated C-terminally to residue R2261. C-terminal stretches after L2259 in chain A and R2261 in chain B 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 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0S3L5
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

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.34 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Hepes, Tacsimate, PEGMME5000

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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: Mar 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.5→130.67 Å / Num. obs: 23225 / % possible obs: 99.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 197.83 Å2 / Rmerge(I) obs: 0.274 / Net I/σ(I): 6.35
Reflection shellResolution: 4.5→4.82 Å / Redundancy: 6.5 % / Rmerge(I) obs: 2.26 / Mean I/σ(I) obs: 1 / % possible all: 99.6

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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

5i6f


Resolution: 4.5→49.1 Å / Cor.coef. Fo:Fc: 0.9228 / Cor.coef. Fo:Fc free: 0.9207 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.885
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 1112 4.76 %RANDOM
Rwork0.2356 ---
obs0.2358 23340 99.42 %-
Displacement parametersBiso mean: 275.06 Å2
Baniso -1Baniso -2Baniso -3
1--72.1696 Å20 Å20 Å2
2--50.9309 Å20 Å2
3---21.2386 Å2
Refine analyzeLuzzati coordinate error obs: 0.976 Å
Refinement stepCycle: LAST / Resolution: 4.5→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16405 0 0 0 16405
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116759HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1122697HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7813SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes446HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2415HARMONIC5
X-RAY DIFFRACTIONt_it16759HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion3.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2148SEMIHARMONIC5
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_contact18765SEMIHARMONIC4
LS refinement shellResolution: 4.5→4.7 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2515 116 4.14 %
Rwork0.2644 2686 -
all0.2639 2802 -
obs--99.61 %
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)
117.2146-0.89776.785417.964-4.542413.6440.05361.2838-0.2986-0.5059-0.32910.53320.7536-0.45770.27550.6227-0.2394-0.4559-0.639-0.3688-0.65243.5088-62.8207-14.0368
28.2663-3.4791-2.27039.37370.414613.1448-0.1256-0.90460.5701-0.83710.307-0.96440.97280.0499-0.1813-0.8194-0.15260.4559-0.9119-0.0465-0.911914.7034-39.68672.3726
30.07910.0709-1.06653.48730.51693.60460.1559-0.0820.27631.61340.1680.1469-0.48140.2609-0.32390.38840.10280.2757-0.4435-0.0891-0.3206-13.224-19.283345.3341
45.17980.4694-2.415523.14788.731217.10830.0221-0.31920.19590.063-0.41650.34210.4676-0.51350.39450.82980.32430.30380.0524-0.394-0.1846-17.6485-4.5518132.014
54.5935-0.693-1.23564.9863-2.19235.06720.28340.104-1.10430.60270.3045-0.99220.67270.1735-0.58780.91190.4353-0.24740.7586-0.08730.3053-9.3161-26.4635112.917
60-0.5501-0.7472.5060.99283.892-0.0914-0.6989-0.10271.63270.07450.05110.6663-0.13280.01690.9119-0.06980.4559-0.0439-0.00370.0397-20.5222-37.664960.556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1186 - 1327}
2X-RAY DIFFRACTION2{A|1328 - 1523}
3X-RAY DIFFRACTION3{A|1524 - 2259}
4X-RAY DIFFRACTION4{B|1186 - 1327}
5X-RAY DIFFRACTION5{B|1328 - 1523}
6X-RAY DIFFRACTION6{B|1524 - 2261}

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