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- PDB-5tv6: A. aeolicus BioW with pimelate -

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Basic information

Entry
Database: PDB / ID: 5tv6
TitleA. aeolicus BioW with pimelate
Components6-carboxyhexanoate--CoA ligase
KeywordsLIGASE / Pimeloyl-CoA Ligase / adenylation
Function / homology6-carboxyhexanoate-CoA ligase / 6-carboxyhexanoate-CoA ligase activity / 6-carboxyhexanoate--CoA ligase / 6-carboxyhexanoate--CoA ligase / biotin biosynthetic process / magnesium ion binding / ATP binding / PIMELIC ACID / 6-carboxyhexanoate--CoA ligase
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.456 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 30, 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)55,6814
Polymers55,3612
Non-polymers3202
Water3,315184
1
A: 6-carboxyhexanoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8412
Polymers27,6801
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 6-carboxyhexanoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8412
Polymers27,6801
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.486, 103.194, 113.805
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: 27680.357 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-PML / PIMELIC ACID


Mass: 160.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C7H12O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.66 Å3/Da / Density % sol: 66.42 %
Crystal growTemperature: 280 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-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 31, 2013
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 30059 / % possible obs: 99.8 % / Redundancy: 7.3 % / Net I/σ(I): 20.9
Reflection shellHighest resolution: 2.45 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.456→49.829 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.17
RfactorNum. reflection% reflection
Rfree0.2298 2507 5.08 %
Rwork0.1896 --
obs0.1917 27317 86.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.456→49.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 22 184 4040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093919
X-RAY DIFFRACTIONf_angle_d1.2725246
X-RAY DIFFRACTIONf_dihedral_angle_d16.8412434
X-RAY DIFFRACTIONf_chiral_restr0.062585
X-RAY DIFFRACTIONf_plane_restr0.009665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4564-2.50370.3104570.27921223X-RAY DIFFRACTION40
2.5037-2.55480.3475850.26351525X-RAY DIFFRACTION51
2.5548-2.61030.2729900.23841775X-RAY DIFFRACTION59
2.6103-2.6710.25111290.23152020X-RAY DIFFRACTION68
2.671-2.73780.32191260.24082272X-RAY DIFFRACTION76
2.7378-2.81180.28561080.23812526X-RAY DIFFRACTION84
2.8118-2.89460.2521720.2392705X-RAY DIFFRACTION91
2.8946-2.9880.29081710.24062841X-RAY DIFFRACTION96
2.988-3.09480.28821420.24592962X-RAY DIFFRACTION98
3.0948-3.21870.25481150.21843031X-RAY DIFFRACTION100
3.2187-3.36510.23111480.20353037X-RAY DIFFRACTION100
3.3651-3.54250.23791810.19962961X-RAY DIFFRACTION100
3.5425-3.76440.25141200.17943013X-RAY DIFFRACTION100
3.7644-4.05490.20851890.16432983X-RAY DIFFRACTION100
4.0549-4.46270.19511850.14362974X-RAY DIFFRACTION100
4.4627-5.10790.18151680.13833004X-RAY DIFFRACTION100
5.1079-6.43330.23911780.18292966X-RAY DIFFRACTION100
6.4333-49.83930.17891430.16973004X-RAY DIFFRACTION100

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