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- PDB-5fll: Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW) fro... -

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Basic information

Entry
Database: PDB / ID: 5fll
TitleCrystal structure of the 6-carboxyhexanoate-CoA ligase (BioW) from Bacillus subtilis in complex with a Pimeloyl-adenylate
Components6-CARBOXYHEXANOATE-COA LIGASE
KeywordsLIGASE
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
PYROPHOSPHATE / PIMELOYL-AMP / 6-carboxyhexanoate--CoA ligase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsMoynie, L. / Wang, M. / Campopiano, D.J. / Naismith, J.H.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Using the pimeloyl-CoA synthetase adenylation fold to synthesize fatty acid thioesters.
Authors: Wang, M. / Moynie, L. / Harrison, P.J. / Kelly, V. / Piper, A. / Naismith, J.H. / Campopiano, D.J.
History
DepositionOct 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 13, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)60,78110
Polymers59,3492
Non-polymers1,4328
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-53.5 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.117, 78.105, 165.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 5 - 255 / Label seq-ID: 6 - 256

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.2996, 0.9473, -0.1135), (0.9493, -0.3078, -0.0635), (-0.0951, -0.0888, -0.9915)
Vector: -9.576, 12.1541, -19.0228)

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Components

#1: Protein 6-CARBOXYHEXANOATE-COA LIGASE


Mass: 29674.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53559, 6-carboxyhexanoate-CoA ligase
#2: Chemical ChemComp-WAQ / PIMELOYL-AMP


Mass: 489.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24N5O10P
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 7.5 / Details: 19% PEG 400 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX / Wavelength: 1.54178
DetectorType: RIGAKU CCD / Detector: CCD / Date: Sep 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 28257 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.4
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.9 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→35.35 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.925 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23417 1419 5 %RANDOM
Rwork0.19919 ---
obs0.20098 26785 99.62 %-
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: 41.049 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å20 Å2
2---1.08 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.34→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4030 0 88 99 4217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194242
X-RAY DIFFRACTIONr_bond_other_d0.0030.023941
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9655735
X-RAY DIFFRACTIONr_angle_other_deg0.7793.0059120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73724.029206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4915748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1441528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214725
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02963
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14831 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 105 -
Rwork0.264 1901 -
obs--97.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.6716-7.6418-4.266823.669415.541616.05230.2823-0.22540.3663-0.58040.4515-0.9667-0.630.3666-0.73380.0738-0.07960.01710.20260.0790.1762-6.3727-2.9788-5.574
21.3704-1.09261.32911.9132-0.41453.66010.0079-0.0283-0.0057-0.00810.05090.14-0.1842-0.234-0.05870.0375-0.0320.02050.1664-0.00710.2786-7.6443-6.95021.9198
32.92711.45551.62643.8621.52252.8761-0.0673-0.05940.06530.17350.0624-0.1324-0.29120.09540.0050.08250.020.0260.1489-0.04280.23314.4025-5.355412.2735
43.5382-0.12430.14482.85640.70083.5858-0.01660.0933-0.01010.04170.0549-0.0986-0.0849-0.0679-0.03830.0210.009-0.01140.12-0.00470.20791.4286-9.53719.5406
515.8246-12.5356-12.376218.077112.682119.3378-0.3481-0.42950.19210.35020.39220.23230.08140.2601-0.04410.14040.0239-0.07780.14290.05440.2362-15.256.3946-12.632
637.892425.46813.112543.2106-13.517231.6442-0.13281.90690.94150.723-0.47940.1389-0.32660.75080.61210.72970.00460.15880.72880.09071.2728-0.24141.9201-19.7329
71.2953-0.77390.79191.6866-1.11743.91670.0121-0.0322-0.0311-0.04190.05220.05810.062-0.2618-0.06420.071-0.0018-0.00820.1985-0.00930.3071-19.36926.5155-21.3345
82.09810.85750.02123.92990.98264.37280.05210.15870.0778-0.33270.0957-0.035-0.1101-0.0597-0.14790.12680.0647-0.0080.19770.0080.2397-17.570415.1347-29.3837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 23
2X-RAY DIFFRACTION2A24 - 91
3X-RAY DIFFRACTION3A92 - 164
4X-RAY DIFFRACTION4A165 - 257
5X-RAY DIFFRACTION5B5 - 17
6X-RAY DIFFRACTION6B18 - 23
7X-RAY DIFFRACTION7B24 - 96
8X-RAY DIFFRACTION8B97 - 255

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