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- PDB-2dzd: Crystal structure of the biotin carboxylase domain of pyruvate ca... -

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Basic information

Entry
Database: PDB / ID: 2dzd
TitleCrystal structure of the biotin carboxylase domain of pyruvate carboxylase
Componentspyruvate carboxylase
KeywordsLIGASE / biotin carboxylase / pyruvate carboxylase / bacillus thermodenitrificans
Function / homology
Function and homology information


pyruvate carboxylase activity / gluconeogenesis / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / Rossmann fold - #20 / 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. ...: / Rossmann fold - #20 / 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 / ATP-grasp fold, A domain / Rudiment single hybrid motif / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyruvate carboxylase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKondo, S. / Nakajima, Y. / Sugio, S. / Sueda, S. / Islam, M.N. / Kondo, H.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007
Title: Structure of the biotin carboxylase domain of pyruvate carboxylase from Bacillus thermodenitrificans
Authors: Kondo, S. / Nakajima, Y. / Sugio, S. / Sueda, S. / Islam, M.N. / Kondo, H.
History
DepositionSep 27, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 25, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pyruvate carboxylase
B: pyruvate carboxylase


Theoretical massNumber of molelcules
Total (without water)102,8072
Polymers102,8072
Non-polymers00
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.609, 115.987, 115.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsUnknown, it is not clearly. Maybe the biological assembly part is dimer in asymmetric unit.

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Components

#1: Protein pyruvate carboxylase


Mass: 51403.406 Da / Num. of mol.: 2 / Fragment: biotin carboxylase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / References: UniProt: Q05FZ3, pyruvate carboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 2% PEG 8000, 100mM Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Nov 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.836 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 42671 / Num. obs: 42671 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.088

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Processing

Software
NameClassification
HKL-2000data collection
EPMRphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ULZ

1ulz


Resolution: 2.4→20 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2129 -RANDOM
Rwork0.232 ---
obs-42429 99.8 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7163 0 0 349 7512

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