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- PDB-1on9: Transcarboxylase 12S crystal structure: hexamer assembly and subs... -

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Basic information

Entry
Database: PDB / ID: 1on9
TitleTranscarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core (with hydrolyzed methylmalonyl-coenzyme a bound)
ComponentsMethylmalonyl-CoA carboxyltransferase 12S subunit
KeywordsTRANSFERASE / carboxyl transferase / domain duplication / multienzyme complex / transcarboxylase
Function / homology
Function and homology information


methylmalonyl-CoA carboxytransferase / methylmalonyl-CoA carboxytransferase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / fatty acid biosynthetic process
Similarity search - Function
Acetyl-CoA carboxylase carboxyl transferase, beta subunit / 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 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Acetyl-CoA carboxylase carboxyl transferase, beta subunit / 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 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / METHYLMALONYL-COENZYME A / Methylmalonyl-CoA carboxyltransferase 12S subunit
Similarity search - Component
Biological speciesPropionibacterium freudenreichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsHall, P.R. / Wang, Y.-F. / Rivera-Hainaj, R.E. / Zheng, X. / Pustai-Carey, M. / Carey, P.R. / Yee, V.C.
CitationJournal: Embo J. / Year: 2003
Title: Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core
Authors: Hall, P.R. / Wang, Y.-F. / Rivera-Hainaj, R.E. / Zheng, X. / Pustai-Carey, M. / Carey, P.R. / Yee, V.C.
History
DepositionFeb 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN MMCoA - only a portion of the CoA entity could be modeled.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylmalonyl-CoA carboxyltransferase 12S subunit
B: Methylmalonyl-CoA carboxyltransferase 12S subunit
C: Methylmalonyl-CoA carboxyltransferase 12S subunit
D: Methylmalonyl-CoA carboxyltransferase 12S subunit
E: Methylmalonyl-CoA carboxyltransferase 12S subunit
F: Methylmalonyl-CoA carboxyltransferase 12S subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,62616
Polymers337,9656
Non-polymers5,66110
Water61,0713390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: Methylmalonyl-CoA carboxyltransferase 12S subunit
E: Methylmalonyl-CoA carboxyltransferase 12S subunit
F: Methylmalonyl-CoA carboxyltransferase 12S subunit
hetero molecules

D: Methylmalonyl-CoA carboxyltransferase 12S subunit
E: Methylmalonyl-CoA carboxyltransferase 12S subunit
F: Methylmalonyl-CoA carboxyltransferase 12S subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,40714
Polymers337,9656
Non-polymers5,4428
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area21020 Å2
ΔGint-89 kcal/mol
Surface area118190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.810, 200.020, 145.900
Angle α, β, γ (deg.)90.00, 102.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-7501-

HOH

21A-7525-

HOH

31C-7530-

HOH

41D-4470-

HOH

51F-6248-

HOH

61F-6256-

HOH

DetailsThe biological assembly is a hexamer.

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Components

#1: Protein
Methylmalonyl-CoA carboxyltransferase 12S subunit / Transcarboxylase 12S


Mass: 56327.473 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Propionibacterium freudenreichii (bacteria)
Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q8GBW6, methylmalonyl-CoA carboxytransferase
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-MCA / METHYLMALONYL-COENZYME A / Methylmalonyl-CoA


Mass: 867.607 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C25H40N7O19P3S
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3390 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: MPD, sodium acetate, cadmium chloride, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
119-25 %MPD1reservoir
20.1 Msodium acetate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 18, 1999
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 234797 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 20
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 17439 / Rsym value: 0.202 / % possible all: 69.1
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 69.1 % / Rmerge(I) obs: 0.236

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2→29.55 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: maximum likelihood target using amplitudes. WATERS 1-2 HAVE COORDINATION SPHERES REMINISCENT OF CATIONS, BUT COULD NOT BE DEFINITIVELY IDENTIFIED AS IONS BECAUSE THEIR B-FACTORS ARE NOT ...Details: maximum likelihood target using amplitudes. WATERS 1-2 HAVE COORDINATION SPHERES REMINISCENT OF CATIONS, BUT COULD NOT BE DEFINITIVELY IDENTIFIED AS IONS BECAUSE THEIR B-FACTORS ARE NOT UNREASONABLY LOW COMPARED TO THE SURROUNDING ATOMS, AND THERE ARE NO CORRESPONDING PEAKS IN THE ANOMALOUS DIFFERENCE DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.198 10242 5 %RANDOM
Rwork0.152 ---
all0.155 213350 --
obs0.152 205243 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.669 Å2 / ksol: 0.337893 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å21 Å2
2--1.01 Å20 Å2
3---1.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23308 0 171 3390 26869
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it2.341.5
X-RAY DIFFRACTIONc_mcangle_it2.792
X-RAY DIFFRACTIONc_scbond_it3.542
X-RAY DIFFRACTIONc_scangle_it4.712.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.221 1678 4.9 %
Rwork0.161 32677 -
obs-34355 96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMLIG.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4MCA.PAR
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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