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- PDB-7kct: Crystal Structure of the Hydrogenobacter thermophilus 2-Oxoglutar... -

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Basic information

Entry
Database: PDB / ID: 7kct
TitleCrystal Structure of the Hydrogenobacter thermophilus 2-Oxoglutarate Carboxylase (OGC) Biotin Carboxylase (BC) Domain Dimer in Complex with Adenosine 5'-Diphosphate Magnesium Salt (MgADP), Adenosine 5'-Diphosphate (ADP, and Bicarbonate Anion (Hydrogen Carbonate/HCO3-)
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. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain ...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 / BICARBONATE ION / 2-oxoglutarate carboxylase small subunit
Similarity search - Component
Biological speciesHydrogenobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
Model detailsNucleotide free dimer with Open Lid domain
AuthorsBuhrman, G.K. / Rose, R.B. / Enriquez, P. / Truong, V.
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 7, 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)111,1739
Polymers109,3552
Non-polymers1,8187
Water5,585310
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)72.282, 86.878, 86.105
Angle α, β, γ (deg.)90.000, 113.649, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 54677.477 Da / Num. of mol.: 2
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 (E. coli) / References: UniProt: D3DJ42, 2-oxoglutarate carboxylase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M sodium malonate pH 5.0 and 12% w/v PEG 3,350

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 61051 / % possible obs: 90 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.22 Å2 / Rsym value: 0.149 / Net I/σ(I): 36.33
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.92 / Num. unique obs: 2567 / Rsym value: 0.221 / % possible all: 61.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KBL

7kbl


Resolution: 2.02→42.1 Å / SU ML: 0.2083 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 2014 3.33 %random selectio
Rwork0.1739 58538 --
obs0.176 60552 94.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.95 Å2
Refinement stepCycle: LAST / Resolution: 2.02→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6959 0 114 310 7383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01677228
X-RAY DIFFRACTIONf_angle_d1.58739811
X-RAY DIFFRACTIONf_chiral_restr0.07771087
X-RAY DIFFRACTIONf_plane_restr0.00941244
X-RAY DIFFRACTIONf_dihedral_angle_d19.17782639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.070.29111240.20423709X-RAY DIFFRACTION84.56
2.07-2.130.25621420.19884117X-RAY DIFFRACTION93.17
2.13-2.190.24141400.18434178X-RAY DIFFRACTION94.65
2.19-2.260.24031470.18134122X-RAY DIFFRACTION93.6
2.26-2.340.23231400.17924077X-RAY DIFFRACTION92.93
2.34-2.430.20681430.17994058X-RAY DIFFRACTION91.87
2.43-2.540.23511330.19423913X-RAY DIFFRACTION88.61
2.54-2.680.25461450.18584152X-RAY DIFFRACTION94.01
2.68-2.850.23361510.18044383X-RAY DIFFRACTION99.47
2.85-3.070.22771500.18964385X-RAY DIFFRACTION99.28
3.07-3.370.24511450.18354366X-RAY DIFFRACTION98.24
3.37-3.860.22531550.16564279X-RAY DIFFRACTION96.54
3.86-4.860.18591480.14114369X-RAY DIFFRACTION97.52
4.86-42.110.17171510.16734430X-RAY DIFFRACTION97.95

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