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- PDB-1on3: Transcarboxylase 12S crystal structure: hexamer assembly and subs... -

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Basic information

Entry
Database: PDB / ID: 1on3
TitleTranscarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core (with methylmalonyl-coenzyme a and methylmalonic acid 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
: / METHYLMALONIC ACID / METHYLMALONYL-COENZYME A / Methylmalonyl-CoA carboxyltransferase 12S subunit
Similarity search - Component
Biological speciesPropionibacterium freudenreichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 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 26, 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: 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_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

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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)344,57124
Polymers337,9656
Non-polymers6,60618
Water60,5843363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53420 Å2
ΔGint-356 kcal/mol
Surface area93330 Å2
MethodPISA
2
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

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)689,14248
Polymers675,93012
Non-polymers13,21236
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area109540 Å2
ΔGint-722 kcal/mol
Surface area183960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.805, 200.708, 146.347
Angle α, β, γ (deg.)90.00, 102.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-7426-

HOH

21C-7517-

HOH

31D-5269-

HOH

41F-6281-

HOH

DetailsThe biological assembly is a hexamer.

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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

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Non-polymers , 5 types, 3381 molecules

#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-DXX / METHYLMALONIC ACID / Methylmalonic acid


Mass: 118.088 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3363 / 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: 2.43 Å3/Da / Density % sol: 49.49 %
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: NSLS / Beamline: X9B / Wavelength: 1.04 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 25, 2002 / Details: Monochromator, mirrors
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 663843 / Num. obs: 240569 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.057 / Net I/σ(I): 3.59
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 24491 / Rsym value: 0.268 / % possible all: 97.4
Reflection
*PLUS
Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 97.4 % / Rmerge(I) obs: 0.268

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→19.97 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 1-6 HAVE COORDINATION SPHERES REMINISCENT OF CATIONS, BUT COULD NOT BE DEFINITIVELY IDENTIFIED AS IONS BECAUSE THEIR B-FACTORS, ALTHOUGH ...Details: maximum likelihood target using amplitudes. WATERS 1-6 HAVE COORDINATION SPHERES REMINISCENT OF CATIONS, BUT COULD NOT BE DEFINITIVELY IDENTIFIED AS IONS BECAUSE THEIR B-FACTORS, ALTHOUGH LOWER THAN THE SURROUNDING ATOMS, ARE NOT UNREASONABLY LOW, AND THERE WERE NO CORRESPONDING PEAKS IN THE ANOMALOUS DIFFERENCE DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.213 10568 4.6 %RANDOM
Rwork0.168 ---
all0.17 252941 --
obs0.168 228317 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.8356 Å2 / ksol: 0.330544 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å22 Å2
2--0.47 Å20 Å2
3---2.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23482 0 375 3387 27244
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it2.451.5
X-RAY DIFFRACTIONc_mcangle_it2.92
X-RAY DIFFRACTIONc_scbond_it3.442
X-RAY DIFFRACTIONc_scangle_it4.452.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 1327 3.7 %
Rwork0.221 34654 -
obs-35981 85.6 %
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
X-RAY DIFFRACTION5MPD.PAR
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0079
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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