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- PDB-4rcn: Structure and function of a single-chain, multi-domain long-chain... -

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Basic information

Entry
Database: PDB / ID: 4rcn
TitleStructure and function of a single-chain, multi-domain long-chain acyl-coa carboxylase
Componentslong-chain acyl-CoA carboxylase
KeywordsLIGASE / holoenzyme / acyl-CoA carboxylase / protein structure / alpha/beta / carboxylase / CoA binding
Function / homology
Function and homology information


acetyl-CoA carboxylase / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
: / 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 carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation 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 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotin/lipoyl attachment / Single hybrid motif / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
acetyl-CoA carboxylase
Similarity search - Component
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.01 Å
AuthorsTran, T.H. / Tong, L.
CitationJournal: Nature / Year: 2015
Title: Structure and function of a single-chain, multi-domain long-chain acyl-CoA carboxylase.
Authors: Tran, T.H. / Hsiao, Y.S. / Jo, J. / Chou, C.Y. / Dietrich, L.E. / Walz, T. / Tong, L.
History
DepositionSep 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: long-chain acyl-CoA carboxylase
B: long-chain acyl-CoA carboxylase


Theoretical massNumber of molelcules
Total (without water)229,4972
Polymers229,4972
Non-polymers00
Water00
1
A: long-chain acyl-CoA carboxylase
B: long-chain acyl-CoA carboxylase

A: long-chain acyl-CoA carboxylase
B: long-chain acyl-CoA carboxylase

A: long-chain acyl-CoA carboxylase
B: long-chain acyl-CoA carboxylase


Theoretical massNumber of molelcules
Total (without water)688,4916
Polymers688,4916
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Buried area57770 Å2
ΔGint-227 kcal/mol
Surface area209100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.880, 220.880, 220.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein long-chain acyl-CoA carboxylase


Mass: 114748.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: strain ATCC BAA-968 / K-10 / Gene: MAP_2873c / Production host: Escherichia coli (E. coli) / References: UniProt: Q73VY8

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.57 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 7.5
Details: 1.5 M ammonium sulfate, 0.1 M bis tris propane, pH 7.5, under oil, temperature 277K, EVAPORATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2013
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 65399 / Num. obs: 64953 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.01→49.39 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 454716.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3305 5.1 %RANDOM
Rwork0.209 ---
obs0.209 64953 91 %-
all-64953 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7133 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 66.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3.01→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14630 0 0 0 14630
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it2.482.5
X-RAY DIFFRACTIONc_mcangle_it4.114
X-RAY DIFFRACTIONc_scbond_it4.523.5
X-RAY DIFFRACTIONc_scangle_it6.815
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.394 327 5.4 %
Rwork0.333 4868 -
obs-6547 72.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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