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- PDB-5tva: A. aeolicus BioW with AMP and CoA -

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Basic information

Entry
Database: PDB / ID: 5tva
TitleA. aeolicus BioW with AMP and CoA
Components6-carboxyhexanoate--CoA ligase
KeywordsLIGASE / Pimeloyl-CoA Ligase / adenylation
Function / homology
Function and homology information


6-carboxyhexanoate-CoA ligase / 6-carboxyhexanoate-CoA ligase activity / biotin biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
6-carboxyhexanoate--CoA ligase / 6-carboxyhexanoate--CoA ligase
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / COENZYME A / 6-carboxyhexanoate--CoA ligase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsEstrada, P. / Manandhar, M. / Dong, S.-H. / Deveryshetty, J. / Agarwal, V. / Cronan, J.E. / Nair, S.K.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: The pimeloyl-CoA synthetase BioW defines a new fold for adenylate-forming enzymes.
Authors: Estrada, P. / Manandhar, M. / Dong, S.H. / Deveryshetty, J. / Agarwal, V. / Cronan, J.E. / Nair, S.K.
History
DepositionNov 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3May 31, 2017Group: Database references
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-carboxyhexanoate--CoA ligase
B: 6-carboxyhexanoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3545
Polymers54,8922
Non-polymers1,4623
Water1,964109
1
A: 6-carboxyhexanoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5613
Polymers27,4461
Non-polymers1,1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 6-carboxyhexanoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7932
Polymers27,4461
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.660, 68.860, 156.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 6-carboxyhexanoate--CoA ligase / Pimeloyl-CoA synthase / BioW


Mass: 27445.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: bioW, aq_1659 / Production host: Escherichia coli (E. coli) / References: UniProt: O67575, 6-carboxyhexanoate-CoA ligase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / Details: 20-30$ PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 29328 / % possible obs: 99.9 % / Redundancy: 8 % / Net I/σ(I): 18.5
Reflection shellHighest resolution: 2.25 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→38.072 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.84
RfactorNum. reflection% reflection
Rfree0.245 1466 5 %
Rwork0.2006 --
obs0.2028 29312 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→38.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 94 109 4029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093990
X-RAY DIFFRACTIONf_angle_d1.1355364
X-RAY DIFFRACTIONf_dihedral_angle_d16.6752443
X-RAY DIFFRACTIONf_chiral_restr0.08596
X-RAY DIFFRACTIONf_plane_restr0.005666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2501-2.33050.30331430.26412726X-RAY DIFFRACTION100
2.3305-2.42380.31351440.24842737X-RAY DIFFRACTION100
2.4238-2.53410.32311450.25472754X-RAY DIFFRACTION100
2.5341-2.66770.32291440.23482736X-RAY DIFFRACTION100
2.6677-2.83480.27641440.22922744X-RAY DIFFRACTION100
2.8348-3.05360.26541470.22152786X-RAY DIFFRACTION100
3.0536-3.36070.25071450.22182759X-RAY DIFFRACTION100
3.3607-3.84660.25591490.19212816X-RAY DIFFRACTION100
3.8466-4.84470.19331480.1652824X-RAY DIFFRACTION100
4.8447-38.0770.22691570.18752964X-RAY DIFFRACTION100

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