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- PDB-5i6f: Crystal structure of C-terminal variant 1 of Chaetomium thermophi... -

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Basic information

Entry
Database: PDB / ID: 5i6f
TitleCrystal structure of C-terminal variant 1 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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 13, 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)266,9092
Polymers266,9092
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13940 Å2
ΔGint-108 kcal/mol
Surface area93430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.660, 165.340, 219.230
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


Mass: 133454.484 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 E2264. 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 E2264. C-terminal stretches after E2264 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: 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: 3.28 Å3/Da / Density % sol: 62.48 %
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: May 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→49.24 Å / Num. obs: 41802 / % possible obs: 99.7 % / Redundancy: 12.7 % / Biso Wilson estimate: 140.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Net I/σ(I): 10.61
Reflection shellResolution: 3.6→3.69 Å / Redundancy: 13.5 % / Rmerge(I) obs: 3.85 / Mean I/σ(I) obs: 0.97 / % 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: homology models of 1od2 and 5i6e

1od2

5i6e


Resolution: 3.6→49.24 Å / Cor.coef. Fo:Fc: 0.9425 / Cor.coef. Fo:Fc free: 0.9219 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.535
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2011 4.81 %RANDOM
Rwork0.2027 ---
obs0.2047 41799 99.75 %-
Displacement parametersBiso mean: 226.33 Å2
Baniso -1Baniso -2Baniso -3
1--57.2406 Å20 Å20 Å2
2--49.3911 Å20 Å2
3---7.8495 Å2
Refine analyzeLuzzati coordinate error obs: 0.584 Å
Refinement stepCycle: LAST / Resolution: 3.6→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16592 0 0 0 16592
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00916944HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0722950HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7892SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes448HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2448HARMONIC5
X-RAY DIFFRACTIONt_it16944HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.34
X-RAY DIFFRACTIONt_other_torsion3.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2182SEMIHARMONIC5
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_contact18849SEMIHARMONIC4
LS refinement shellResolution: 3.6→3.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2628 124 4.08 %
Rwork0.2682 2914 -
all0.268 3038 -
obs--99.93 %
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)
16.31682.13341.76437.3699-1.44637.0778-0.00360.0103-0.01810.0147-0.0052-0.0547-0.00460.02810.00880.36030.03-0.11060.22790.08980.2035110.854165.271125.341
24.1238-1.6452-1.46256.4031-4.90415.72480.006-0.10890.12310.04540.05990.1169-0.0854-0.0505-0.06590.46190.0641-0.02090.29410.1329-0.171998.4405190.318112.563
31.3206-1.31570.26117.43841.42518.64550.0358-0.34110.06811.08190.4624-0.15160.74150.1328-0.4982-0.0989-0.001-0.3034-0.5230.0821-0.1846109.938205.90561.2041
45.591-2.9407-1.37078.3564-0.95818.070.00140.05740.0152-0.0502-0.0159-0.0218-0.0229-0.02540.01440.3317-0.0302-0.07790.2098-0.01890.218995.2892226.929-18.2136
513.559-1.4771.31641.77520.231311.9064-0.0251-0.2220.10120.1120.10970.1733-0.1413-0.2312-0.08470.14750.1631-0.19630.40320.0443-0.187282.0278206.7010.5867
62.20881.2887011.6567-0.97584.55420.0849-0.0034-0.29071.07320.1742-0.22820.59130.0245-0.2591-0.46430.0863-0.1055-0.39340.0755-0.2894106.888186.83546.0275
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 - 2264}
4X-RAY DIFFRACTION4{B|1186 - 1327}
5X-RAY DIFFRACTION5{B|1328 - 1523}
6X-RAY DIFFRACTION6{B|1524 - 2264}

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