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- PDB-8hz5: The homodimer of a biotin carboxylase isoform from chloroflexus a... -

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Basic information

Entry
Database: PDB / ID: 8hz5
TitleThe homodimer of a biotin carboxylase isoform from chloroflexus aurantiacus
ComponentsBiotin carboxylase
KeywordsLIGASE / Biotin carboxylase / Chloroflexus aurantiacus / Acetyl-CoA carboxylase / 3-hydroxypropionate cycle
Function / homology
Function and homology information


biotin carboxylase / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Acetyl-CoA carboxylase, biotin carboxylase / Phosphoribosylglycinamide synthetase, ATP-grasp (A) 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 / Carbamoyl-phosphate synthase subdomain signature 1. ...Acetyl-CoA carboxylase, biotin carboxylase / Phosphoribosylglycinamide synthetase, ATP-grasp (A) 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 / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Rudiment single hybrid motif / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShen, J. / Wu, W. / Xu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870740, 32171227, 31570738, 32000034, 82101628 China
CitationJournal: To be published
Title: The homodimer of a biotin carboxylase isoform from chloroflexus aurantiacus
Authors: Shen, J. / Wu, W. / Xu, X.
History
DepositionJan 8, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 2.0Mar 20, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biotin carboxylase
B: Biotin carboxylase


Theoretical massNumber of molelcules
Total (without water)102,4462
Polymers102,4462
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.790, 154.092, 206.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Biotin carboxylase / / Acetyl-coenzyme A carboxylase biotin carboxylase subunit A


Mass: 51223.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
Gene: Caur_3421 / Production host: Escherichia coli (E. coli) / References: UniProt: A9WKH8, biotin carboxylase
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 28% (v/v) isopropyl alcohol, 0.1M Bis-Tris pH 6.5, 4% (v/v) PEG200
PH range: 7.8-8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3→24.06 Å / Num. obs: 17211 / % possible obs: 95.4 % / Redundancy: 11.5 % / CC1/2: 0.884 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 1678 / CC1/2: 0.777

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
HKL-3000723data scaling
HKL-3000723data reduction
PHASER1.19.2-4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→23.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2864 814 -
Rwork0.2446 --
obs-17209 95.41 %
Refinement stepCycle: LAST / Resolution: 3→23.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5445 0 4 0 5449
LS refinement shellResolution: 3→3.107 Å
RfactorNum. reflection% reflection
Rfree0.3675 --
Rwork0.2863 --
obs-1679 95.45 %

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