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- PDB-6akd: Crystal structure of IdnL7 -

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Basic information

Entry
Database: PDB / ID: 6akd
TitleCrystal structure of IdnL7
ComponentsAMP-dependent synthetase and ligase
KeywordsLIGASE / ATP-binding / five layered alpha-beta-alpha-beta-alpha sandwich fold
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / cytoplasm
Similarity search - Function
ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE / AMP-dependent synthetase and ligase
Similarity search - Component
Biological speciesStreptomyces sp. ML694-90F3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCieslak, J. / Miyanaga, A. / Kudo, F. / Eguchi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25850050 Japan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: Functional and structural characterization of IdnL7, an adenylation enzyme involved in incednine biosynthesis.
Authors: Cieslak, J. / Miyanaga, A. / Takaishi, M. / Kudo, F. / Eguchi, T.
History
DepositionAug 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: 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: AMP-dependent synthetase and ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1164
Polymers57,5151
Non-polymers6023
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-2 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.526, 68.526, 225.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein AMP-dependent synthetase and ligase


Mass: 57514.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. ML694-90F3 (bacteria) / Strain: ML694-90F / Gene: idnL7 / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: A0A077KUW8
#2: Chemical ChemComp-A5A / '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE


Mass: 417.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N7O7S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Tris, 0.2M magnesium chloride, 30% PEG4000, 0.5mM [N-(L-alanyl)sulfamoyl] adenosine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 2, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 32390 / % possible obs: 99.7 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 33.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1587 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AMU

1amu


Resolution: 2.1→43.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.933 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.168 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22031 1642 5.1 %RANDOM
Rwork0.17732 ---
obs0.17946 30667 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.169 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å20 Å2
2--0.3 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 2.1→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3682 0 40 155 3877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193810
X-RAY DIFFRACTIONr_bond_other_d0.0010.023612
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.9785197
X-RAY DIFFRACTIONr_angle_other_deg0.88538254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2485481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97421.566166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93915532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5771545
X-RAY DIFFRACTIONr_chiral_restr0.1090.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02890
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
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 133 -
Rwork0.229 2209 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 4.514 Å / Origin y: 20.613 Å / Origin z: 67.172 Å
111213212223313233
T0.0142 Å20.014 Å2-0.0249 Å2-0.0855 Å2-0.0088 Å2--0.1144 Å2
L0.7972 °2-0.0757 °20.0128 °2-0.8292 °2-0.3853 °2--1.4129 °2
S0.0295 Å °0.0152 Å °0.1278 Å °-0.0771 Å °-0.0672 Å °0.1388 Å °-0.0226 Å °0.1304 Å °0.0377 Å °

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