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- PDB-5i6h: Crystal structure of CD-CT domains of Chaetomium thermophilum ace... -

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Basic information

Entry
Database: PDB / ID: 5i6h
TitleCrystal structure of CD-CT domains of Chaetomium thermophilum acetyl-CoA carboxylase
ComponentsAcetyl-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, 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 / 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: 7.2 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 1.3Oct 9, 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
B: Acetyl-CoA carboxylase-like protein


Theoretical massNumber of molelcules
Total (without water)338,6602
Polymers338,6602
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14120 Å2
ΔGint-106 kcal/mol
Surface area125220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)295.020, 295.020, 189.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Acetyl-CoA carboxylase-like protein


Mass: 169330.062 Da / Num. of mol.: 2
Fragment: CD-CT domains,CD-CT domains,CD-CT domains,CD-CT domains,CD-CT domains,CD-CT domains,CD-CT domains,CD-CT domains
Source method: isolated from a genetically manipulated source
Details: The crystallized construct contains amino acids 787-2297 (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 787-2297 (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 / 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

Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Bicine, PEG8000

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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: Sep 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 7.2→49.85 Å / Num. obs: 14050 / % possible obs: 99.6 % / Redundancy: 9.9 % / Biso Wilson estimate: 749.32 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.95
Reflection shellResolution: 7.2→7.39 Å / Redundancy: 10.4 % / Rmerge(I) obs: 3.03 / Mean I/σ(I) obs: 0.92 / % possible all: 100

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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: 7.2→49.85 Å / Cor.coef. Fo:Fc: 0.7578 / Cor.coef. Fo:Fc free: 0.7313 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 2.194
RfactorNum. reflection% reflectionSelection details
Rfree0.248 696 4.96 %RANDOM
Rwork0.2322 ---
obs0.233 14046 99.93 %-
Displacement parametersBiso mean: 271.59 Å2
Baniso -1Baniso -2Baniso -3
1-18.1805 Å20 Å20 Å2
2--18.1805 Å20 Å2
3----36.361 Å2
Refine analyzeLuzzati coordinate error obs: 0.87 Å
Refinement stepCycle: LAST / Resolution: 7.2→49.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22543 0 0 0 22543
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123015HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1531159HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10815SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes620HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3309HARMONIC5
X-RAY DIFFRACTIONt_it23015HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion3.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2928SEMIHARMONIC5
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_contact26813SEMIHARMONIC4
LS refinement shellResolution: 7.2→7.78 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2691 133 4.65 %
Rwork0.2468 2730 -
all0.2479 2863 -
obs--99.72 %
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)
117.38484.36569.318832.5078-4.701724.9463-0.372-0.1176-0.049-1.13230.72870.1586-1.2861-0.295-0.35670.5170.2280.23941.30680.34990.9119-177.173317.7851-15.2924
217.70527.4846-0.731820.7016-4.940324.94630.2011-0.9794-1.19391.8441-0.2222-0.25681.24720.71150.02110.25320.07570.1441.21880.10870.9118-142.73179.098613.0046
39.577-0.5568-7.72888.09-4.07589.45390.20990.07420.28140.09470.2231.269-0.5016-1.5223-0.4329-0.9722-0.34890.43090.48330.1656-0.0438-135.5626-2.5587-12.6502
41.76-0.28770.40664.8999-1.25990.44670.5318-0.1045-1.05260.3110.49010.78970.6496-0.2442-1.0219-0.517-0.228-0.3604-1.30680.3184-0.9119-87.0308-24.2935-27.0359
522.13981.62036.893227.7528-6.102224.94630.2662-1.1159-0.277-0.2895-0.31150.4530.30292.05750.04521.3068-0.228-0.62240.5170.16610.9119-44.7118-129.7208-17.5791
626.04450.99347.069518.2106-5.998724.92980.07021.43240.5364-1.81150.27830.9058-0.5969-1.0769-0.34861.0048-0.2988-0.5340.2990.0130.9119-51.6702-92.2866-44.7774
75.62033.41520.157221.8406-6.43745.42690.1219-0.7764-1.46770.9984-0.0996-0.0381.68170.3023-0.0224-0.4731-0.2027-0.3979-1.29190.2967-0.3588-55.2919-83.3021-17.8805
82.2335-1.24510.29516.8246-0.62693.85260.3954-1.354-1.6761.85910.1643-0.3486-0.4999-0.5278-0.5597-0.4656-0.3171-0.6228-1.15230.1669-0.9119-74.4987-32.55-7.1382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|788 - 1032}
2X-RAY DIFFRACTION2{A|1036 - 1327}
3X-RAY DIFFRACTION3{A|1328 - 1523}
4X-RAY DIFFRACTION4{A|1524 - 2297}
5X-RAY DIFFRACTION5{B|788 - 1032}
6X-RAY DIFFRACTION6{B|1036 - 1327}
7X-RAY DIFFRACTION7{B|1328 - 1523}
8X-RAY DIFFRACTION8{B|1524 - 2297}

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