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- PDB-5fm0: Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from... -

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Basic information

Entry
Database: PDB / ID: 5fm0
TitleCrystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from Bacillus subtilis (PtCl4 derivative)
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 / SYNCHROTRON / SAD / Resolution: 2.44 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 29, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3May 24, 2017Group: Database references
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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)61,90314
Polymers59,3492
Non-polymers2,55412
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-163.4 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.610, 78.360, 166.700
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: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 6 - 255 / Label seq-ID: 7 - 256

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

NCS oper: (Code: given
Matrix: (0.2919, 0.9526, -0.0862), (0.9491, -0.2996, -0.0973), (-0.1185, -0.0534, -0.9915)
Vector: 44.4045, -63.1652, -18.3507)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 6-CARBOXYHEXANOATE--COA LIGASE / PIMELOYL-COA SYNTHASE


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

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Non-polymers , 5 types, 30 molecules

#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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Pt
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 0.1 MM HEPES PH 7.5 19 % PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.07206
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07206 Å / Relative weight: 1
ReflectionResolution: 2.44→83.35 Å / Num. obs: 25521 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 15.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.3
Reflection shellResolution: 2.44→2.5 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.44→83.35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.936 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24214 1298 5.1 %RANDOM
Rwork0.1983 ---
obs0.20052 24163 99.92 %-
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: 56.428 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å20 Å20 Å2
2---2.67 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.44→83.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3971 0 92 18 4081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194168
X-RAY DIFFRACTIONr_bond_other_d0.0040.023896
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9675632
X-RAY DIFFRACTIONr_angle_other_deg0.7723.0059009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8785494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76523.92199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3715739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2351528
X-RAY DIFFRACTIONr_chiral_restr0.0710.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214616
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02944
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: 14996 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 89 -
Rwork0.371 1761 -
obs--99.95 %

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