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- PDB-8hz4: The tetrameric structure of biotin carboxylase from Chloroflexus ... -

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Basic information

Entry
Database: PDB / ID: 8hz4
TitleThe tetrameric structure of biotin carboxylase from Chloroflexus aurantiacus in complex with bicarbonate
Components(Biotin carboxylase) x 2
KeywordsLIGASE / biotin carboxylase / biotin carboxyl carrier protein / 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 / Biotin-binding site / Biotin-requiring enzymes attachment site. / 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 ...Acetyl-CoA carboxylase, biotin carboxylase / Biotin-binding site / Biotin-requiring enzymes attachment site. / 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 synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / 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: 3.2 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 tetrameric structure of biotin carboxylase from Chloroflexus aurantiacus in complex with bicarbonate
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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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
C: Biotin carboxylase
D: Biotin carboxylase
E: Biotin carboxylase
F: Biotin carboxylase
G: Biotin carboxylase
H: Biotin carboxylase


Theoretical massNumber of molelcules
Total (without water)262,3668
Polymers262,3668
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.528, 126.224, 132.192
Angle α, β, γ (deg.)90.00, 106.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 51342.344 Da / Num. of mol.: 4 / Fragment: N-terminal BC domain
Source method: isolated from a genetically manipulated source
Details: Author stated: Chloroflexus aurantiacus Biotin carboxylase (WP_012257262) is a polypeptide containing 596 amino acids, which is composed of an N-terminal BC domain (Met1-Glu452) and C- ...Details: Author stated: Chloroflexus aurantiacus Biotin carboxylase (WP_012257262) is a polypeptide containing 596 amino acids, which is composed of an N-terminal BC domain (Met1-Glu452) and C-terminal biotin carboxyl carrier domain (BCCP, Ala459-Lys596). However, the crystal structure resolved two homodimers in one asymmetric unit. Each monomer contains the intact BC domain (with chain ID A/B/C/D, length 474), but only partial of the BCCP domain (Arg470-Gly487) was resolved in the crystal structure. A long flexible linker between the BC and BCCP domains are invisible due to lack of clear electron density. It is difficult to distinguish the resolved BCCP domain (Arg470-Gly487) belonging to which chain of the BC domain. For accuracy, we assign the chain ID chain E/F/G/H for the resolved BCCP domain (Arg470-Gly487) in the coordinates.
Source: (gene. exp.) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
Gene: Caur_1378 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9W9X0, biotin carboxylase
#2: Protein
Biotin carboxylase / / Acetyl-coenzyme A carboxylase biotin carboxylase subunit A


Mass: 14249.106 Da / Num. of mol.: 4 / Fragment: BCCP-lile domain
Source method: isolated from a genetically manipulated source
Details: Author stated: In the Genome of Chloroflexus aurantiacus, Biotin carboxylase (WP_012257262) is composed of BC and BCCP domains. In our tetrameric biotin carboxylase structure, BC and BCCP ...Details: Author stated: In the Genome of Chloroflexus aurantiacus, Biotin carboxylase (WP_012257262) is composed of BC and BCCP domains. In our tetrameric biotin carboxylase structure, BC and BCCP domains are separated due to the poor electronic density of the flexible linker between the two domains. This "separation" confuses us to distinguish which two incomplete chains belong to the same chain. So, we have recoded the new chain for BCCP domain which are chain E,F, G, H.
Source: (gene. exp.) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
Gene: Caur_1378 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9W9X0, 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: 3.79 Å3/Da / Density % sol: 67.55 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Bicine pH 9.0, 2% (v/v) 1,4-Dioxane, 10% (w/v) PEG20,000, 5% (w/v) PEG550
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: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→28.8 Å / Num. obs: 66529 / % possible obs: 99.22 % / Redundancy: 6.7 % / CC1/2: 0.895 / Net I/σ(I): 4.5
Reflection shellResolution: 3.2→3.314 Å / Num. unique obs: 6647 / CC1/2: 0.65

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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: 3.2→28.8 Å / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 3184 4.79 %
Rwork0.2124 --
obs0.214 66468 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14386 0 20 0 14406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314712
X-RAY DIFFRACTIONf_angle_d0.68719965
X-RAY DIFFRACTIONf_dihedral_angle_d4.0752088
X-RAY DIFFRACTIONf_chiral_restr0.0462209
X-RAY DIFFRACTIONf_plane_restr0.0072650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.250.35391320.36432737X-RAY DIFFRACTION99
3.25-3.30.38371280.3492777X-RAY DIFFRACTION100
3.3-3.350.31331490.31532717X-RAY DIFFRACTION100
3.35-3.410.31821620.30342752X-RAY DIFFRACTION100
3.41-3.470.33791320.28482733X-RAY DIFFRACTION100
3.47-3.540.30021200.27492774X-RAY DIFFRACTION100
3.54-3.610.29711190.27292760X-RAY DIFFRACTION100
3.61-3.690.27351310.25142764X-RAY DIFFRACTION100
3.69-3.770.25541340.22452765X-RAY DIFFRACTION100
3.77-3.870.22971250.21252759X-RAY DIFFRACTION100
3.87-3.970.22561220.21352762X-RAY DIFFRACTION100
3.97-4.090.25641400.21732759X-RAY DIFFRACTION100
4.09-4.220.23531250.20172759X-RAY DIFFRACTION100
4.22-4.370.22281680.18682760X-RAY DIFFRACTION100
4.37-4.550.20011470.18062736X-RAY DIFFRACTION100
4.55-4.750.2031500.17982752X-RAY DIFFRACTION100
4.75-50.20771450.16942742X-RAY DIFFRACTION100
5-5.310.26241440.18132760X-RAY DIFFRACTION99
5.31-5.720.21671410.19662757X-RAY DIFFRACTION99
5.72-6.290.24041530.19022762X-RAY DIFFRACTION99
6.29-7.190.22381350.18972770X-RAY DIFFRACTION99
7.19-9.010.20371390.16382769X-RAY DIFFRACTION99
9.01-28.80.23411430.1932658X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 59.3023 Å / Origin y: -18.4379 Å / Origin z: 171.3322 Å
111213212223313233
T0.5589 Å20.0041 Å2-0.0419 Å2-0.414 Å20.015 Å2--0.5458 Å2
L0.2369 °20.0128 °2-0.0385 °2--0.0428 °20.0193 °2--0.1499 °2
S0.0145 Å °0.0525 Å °-0.0305 Å °-0.0671 Å °-0.0294 Å °0.0588 Å °-0.0263 Å °0.0072 Å °0.0138 Å °
Refinement TLS groupSelection details: all

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