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- PDB-7kbl: Biotin Carboxylase domain of Thermophilic 2-Oxoglutarate Carboxyl... -

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Basic information

Entry
Database: PDB / ID: 7kbl
TitleBiotin Carboxylase domain of Thermophilic 2-Oxoglutarate Carboxylase bound to Bicarbonate
Components2-oxoglutarate carboxylase small subunit
KeywordsLIGASE / biotin carboxylase / biotin-dependent carboxylase / pyruvate carboxylase / ATP-grasp / Aquificales / rTCA / dimer interface / bicarbonate / Sequence Determining Positions / structural waters / thermophile / carbon fixation / thermophilic protein / dimer / wet interface
Function / homology
Function and homology information


2-oxoglutarate carboxylase / 2-oxoglutarate carboxylase activity / ATP binding / metal ion binding
Similarity search - Function
Acetyl-CoA carboxylase, biotin carboxylase / : / 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 / : / 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
BICARBONATE ION / 2-oxoglutarate carboxylase small subunit
Similarity search - Component
Biological speciesHydrogenobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Model detailsNucleotide free dimer with Open Lid domain
AuthorsBuhrman, G.K. / Rose, R.B. / Enriquez, P. / Truong, V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AR0000207 United States
CitationJournal: Biochemistry / Year: 2021
Title: Structure, Function, and Thermal Adaptation of the Biotin Carboxylase Domain Dimer from Hydrogenobacter thermophilus 2-Oxoglutarate Carboxylase.
Authors: Buhrman, G. / Enriquez, P. / Dillard, L. / Baer, H. / Truong, V. / Grunden, A.M. / Rose, R.B.
History
DepositionOct 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-oxoglutarate carboxylase small subunit
B: 2-oxoglutarate carboxylase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3634
Polymers109,2412
Non-polymers1222
Water6,413356
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)67.496, 125.154, 125.949
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 437 or (resid 438...
21(chain B and (resid 1 through 33 or (resid 34...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHR(chain A and (resid 1 through 437 or (resid 438...AA1 - 43710 - 446
12ARGARGARGARG(chain A and (resid 1 through 437 or (resid 438...AA438447
13ALAALAALAALA(chain A and (resid 1 through 437 or (resid 438...AA0 - 4509 - 459
14ALAALAALAALA(chain A and (resid 1 through 437 or (resid 438...AA0 - 4509 - 459
15ALAALAALAALA(chain A and (resid 1 through 437 or (resid 438...AA0 - 4509 - 459
16ALAALAALAALA(chain A and (resid 1 through 437 or (resid 438...AA0 - 4509 - 459
21METMETASNASN(chain B and (resid 1 through 33 or (resid 34...BB1 - 3310 - 42
22GLUGLUGLUGLU(chain B and (resid 1 through 33 or (resid 34...BB3443
23METMETGLUGLU(chain B and (resid 1 through 33 or (resid 34...BB1 - 45110 - 460
24METMETGLUGLU(chain B and (resid 1 through 33 or (resid 34...BB1 - 45110 - 460
25METMETGLUGLU(chain B and (resid 1 through 33 or (resid 34...BB1 - 45110 - 460

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Components

#1: Protein 2-oxoglutarate carboxylase small subunit / 2-oxoglutarate carboxylase beta subunit


Mass: 54620.426 Da / Num. of mol.: 2 / Fragment: Biotin Carboxylase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria)
Gene: cfiB, HTH_1393, Hydth_1383 / Plasmid: pQE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3DJ42, 2-oxoglutarate carboxylase
#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, 0.02M Citric Acid, 0.08M Bis-Tris-Propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→30 Å / Num. obs: 51900 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 33.71 Å2 / Rsym value: 0.125 / Net I/σ(I): 20.8
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 5.4 % / Num. unique obs: 2693 / Rsym value: 0.58 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1ULZ

1ulz


Resolution: 2.3→29.746 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 1758 3.66 %
Rwork0.1814 46289 -
obs0.1833 48047 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.2 Å2 / Biso mean: 43.5904 Å2 / Biso min: 22.02 Å2
Refinement stepCycle: final / Resolution: 2.3→29.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6941 0 10 356 7307
Biso mean--33.03 39.01 -
Num. residues----894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137088
X-RAY DIFFRACTIONf_angle_d1.1589592
X-RAY DIFFRACTIONf_chiral_restr0.0611055
X-RAY DIFFRACTIONf_plane_restr0.0081245
X-RAY DIFFRACTIONf_dihedral_angle_d16.3934252
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5028X-RAY DIFFRACTION7.56TORSIONAL
12B5028X-RAY DIFFRACTION7.56TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.36220.31571350.24463516100
2.3622-2.43160.31161330.22133519100
2.4316-2.51010.27911320.20933524100
2.5101-2.59980.2591350.19593510100
2.5998-2.70380.27131340.18853512100
2.7038-2.82670.25231370.18843529100
2.8267-2.97560.26121320.1873548100
2.9756-3.16190.26031340.20153540100
3.1619-3.40570.24681360.18833566100
3.4057-3.74780.25271350.1821355599
3.7478-4.28880.21081360.1593582100
4.2888-5.39810.17931370.14663617100
5.3981-29.7460.19371420.1843377199

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