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- PDB-7kc7: Biotin Carboxylase domain of Thermophilic 2-Oxoglutarate Carboxyl... -

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Basic information

Entry
Database: PDB / ID: 7kc7
TitleBiotin Carboxylase domain of Thermophilic 2-Oxoglutarate Carboxylase bound to ADP without Magnesium with disordered phosphate tail
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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / 2-oxoglutarate carboxylase small subunit
Similarity search - Component
Biological speciesHydrogenobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 5, 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
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: 2-oxoglutarate carboxylase small subunit
B: 2-oxoglutarate carboxylase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6475
Polymers110,0302
Non-polymers6173
Water1,982110
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)64.968, 120.489, 124.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 55014.836 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: pET24b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3DJ42, 2-oxoglutarate carboxylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
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: 2.2→50 Å / Num. obs: 50075 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 40.77 Å2 / Rsym value: 0.112 / Net I/σ(I): 26.54
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.9 % / Num. unique obs: 2489 / Rsym value: 1.29 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1ULZ

1ulz


Resolution: 2.2→44.17 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 2005 4.01 %
Rwork0.1752 47994 -
obs0.1773 49999 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.59 Å2 / Biso mean: 52.3385 Å2 / Biso min: 24.18 Å2
Refinement stepCycle: final / Resolution: 2.2→44.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6999 0 24 110 7133
Biso mean--59.36 42.62 -
Num. residues----902
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.250.32261310.24823062319389
2.25-2.310.26221400.217134073547100
2.31-2.380.26961430.202733953538100
2.38-2.460.27911500.19734093559100
2.46-2.540.28681380.187334143552100
2.54-2.650.24371510.175234333584100
2.65-2.770.25761390.184834313570100
2.77-2.910.23491410.182934313572100
2.91-3.090.25381450.19434553600100
3.09-3.330.27051440.185634363580100
3.33-3.670.20781390.17734873626100
3.67-4.20.20551460.154834603606100
4.2-5.290.18741460.14553525367199
5.29-44.170.21481520.17873649380199

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