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- PDB-1pix: Crystal structure of the carboxyltransferase subunit of the bacte... -

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Basic information

Entry
Database: PDB / ID: 1pix
TitleCrystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase
ComponentsGlutaconyl-CoA decarboxylase A subunit
KeywordsLYASE / decarboxylase / biotin-dependent ion pump / carboxyltransferase
Function / homology
Function and homology information


glutaconyl-CoA decarboxylase / glutaconyl-CoA decarboxylase activity / glutamate catabolic process via 2-hydroxyglutarate / sodium ion transport / ligase activity
Similarity search - Function
Single Helix bin / Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / 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 ...Single Helix bin / Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Glutaconyl-CoA decarboxylase subunit alpha
Similarity search - Component
Biological speciesAcidaminococcus fermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsWendt, K.S. / Schall, I. / Huber, R. / Buckel, W. / Jacob, U.
CitationJournal: Embo J. / Year: 2003
Title: Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase
Authors: Wendt, K.S. / Schall, I. / Huber, R. / Buckel, W. / Jacob, U.
History
DepositionMay 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Glutaconyl-CoA decarboxylase A subunit
B: Glutaconyl-CoA decarboxylase A subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,51111
Polymers128,8472
Non-polymers6649
Water11,908661
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-136 kcal/mol
Surface area43650 Å2
MethodPISA
2
A: Glutaconyl-CoA decarboxylase A subunit
B: Glutaconyl-CoA decarboxylase A subunit
hetero molecules

A: Glutaconyl-CoA decarboxylase A subunit
B: Glutaconyl-CoA decarboxylase A subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,02322
Polymers257,6944
Non-polymers1,32918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area36360 Å2
ΔGint-305 kcal/mol
Surface area73880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.869, 151.869, 163.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is generated by the two monomers in the asymmetric unit

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Components

#1: Protein Glutaconyl-CoA decarboxylase A subunit / Carboxyltransferase


Mass: 64423.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidaminococcus fermentans (bacteria) / Gene: GCDA / Plasmid: pJF118HE / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q06700, EC: 4.1.1.70
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 3.65 Å3/Da / Density % sol: 66.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: acetate buffer, sodium formate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1500 mM1dropNaCl
2150 mMphosphate1droppH7.5
33 mMTris-HCl1reservoirpH7.0
4500 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 96752 / Num. obs: 95460 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.2→2.21 Å / Rmerge(I) obs: 0.069 / Mean I/σ(I) obs: 13.7 / % possible all: 98.7
Reflection
*PLUS
Highest resolution: 2.2 Å / % possible obs: 99.1 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4780 -random
Rwork0.201 ---
all-96752 --
obs-95460 98.7 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9019 0 25 673 9717
Refinement
*PLUS
Highest resolution: 2.2 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.01
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.3741

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