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- PDB-5h80: Biotin Carboxylase domain of single-chain bacterial carboxylase -

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Basic information

Entry
Database: PDB / ID: 5h80
TitleBiotin Carboxylase domain of single-chain bacterial carboxylase
ComponentsCarboxylase
KeywordsLIGASE / Multienzymes / protein dynamics / X-ray crystallography / small-angle X-ray scattering / carrier protein
Function / homology
Function and homology information


ligase activity / ATP binding / metal ion binding
Similarity search - Function
: / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Rossmann fold - #20 / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain ...: / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Rossmann fold - #20 / 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 / ATP-grasp fold, A domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Dna Ligase; domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHagmann, A. / Hunkeler, M. / Stuttfeld, E. / Maier, T.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation138262 Switzerland
Swiss National Science Foundation159696 Switzerland
Swiss National Science Foundation14523 Switzerland
CitationJournal: Structure / Year: 2016
Title: Hybrid Structure of a Dynamic Single-Chain Carboxylase from Deinococcus radiodurans.
Authors: Hagmann, A. / Hunkeler, M. / Stuttfeld, E. / Maier, T.
History
DepositionDec 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3Jan 10, 2024Group: 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: Carboxylase
B: Carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3389
Polymers105,9032
Non-polymers4347
Water14,160786
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint26 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.100, 138.100, 97.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Carboxylase


Mass: 52951.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_A0310 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9RYK2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 786 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MgCl2 HEPES (pH 7.5) poly(acrylic acid sodium salt) 5,100.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.694
11K, H, -L20.306
ReflectionResolution: 1.7→75.74 Å / Num. obs: 116236 / % possible obs: 99.87 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.61
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 1.18 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DZD

2dzd


Resolution: 1.7→75.74 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.475 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18441 4740 4.1 %RANDOM
Rwork0.14942 ---
obs0.15084 111463 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.312 Å2
Baniso -1Baniso -2Baniso -3
1--11.26 Å2-0 Å2-0 Å2
2---11.26 Å2-0 Å2
3---22.52 Å2
Refinement stepCycle: LAST / Resolution: 1.7→75.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6463 0 28 786 7277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0196649
X-RAY DIFFRACTIONr_bond_other_d0.0020.026382
X-RAY DIFFRACTIONr_angle_refined_deg2.3711.9549061
X-RAY DIFFRACTIONr_angle_other_deg1.266314565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1075855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20523.355304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74115977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6181559
X-RAY DIFFRACTIONr_chiral_restr0.1680.21041
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217700
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021555
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6293.1763435
X-RAY DIFFRACTIONr_mcbond_other3.6283.1753434
X-RAY DIFFRACTIONr_mcangle_it4.5394.7494285
X-RAY DIFFRACTIONr_mcangle_other4.5394.754286
X-RAY DIFFRACTIONr_scbond_it4.3563.5443214
X-RAY DIFFRACTIONr_scbond_other4.3553.5443214
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.925.1634777
X-RAY DIFFRACTIONr_long_range_B_refined8.03427.3767955
X-RAY DIFFRACTIONr_long_range_B_other7.80826.477483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 368 -
Rwork0.291 8109 -
obs--98.31 %

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