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- PDB-8pyy: Amide bond synthetase from Streptomyces hindustanus in open confo... -

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Basic information

Entry
Database: PDB / ID: 8pyy
TitleAmide bond synthetase from Streptomyces hindustanus in open conformation
ComponentsFatty-acyl-CoA synthase
KeywordsLIGASE / Amide / Amide Bond Synthetase / ATP
Function / homology
Function and homology information


ligase activity, forming carbon-sulfur bonds
Similarity search - Function
: / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-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
Fatty-acyl-CoA synthase
Similarity search - Component
Biological speciesStreptoalloteichus hindustanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTang, Q. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/T01430X/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2024
Title: Broad Spectrum Enantioselective Amide Bond Synthetase from Streptoalloteichus hindustanus.
Authors: Tang, Q. / Petchey, M. / Rowlinson, B. / Burden, T.J. / Fairlamb, I.J.S. / Grogan, G.
History
DepositionJul 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty-acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2109
Polymers54,4411
Non-polymers7698
Water90150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-71 kcal/mol
Surface area21920 Å2
Unit cell
Length a, b, c (Å)161.530, 161.530, 162.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Fatty-acyl-CoA synthase


Mass: 54441.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus hindustanus (bacteria)
Gene: SAMN05444320_10350 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M5ABR5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 5.62 Å3/Da / Density % sol: 78.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.8 M Li2SO4; 0.1M bis-tris propane pH 6.5

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.9→57.32 Å / Num. obs: 28308 / % possible obs: 100 % / Redundancy: 40.1 % / Biso Wilson estimate: 48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.34 / Rpim(I) all: 0.05 / Net I/σ(I): 11.3
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 1.93 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4468 / CC1/2: 0.83 / Rpim(I) all: 0.03

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→57.32 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.577 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21379 1403 5 %RANDOM
Rwork0.17464 ---
obs0.17657 26876 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.576 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.9→57.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 40 52 3859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123879
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163631
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.6485305
X-RAY DIFFRACTIONr_angle_other_deg0.5231.5648327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6425499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.559535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53710569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024617
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02855
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_it4.5465.1152002
X-RAY DIFFRACTIONr_mcbond_other4.5145.1162002
X-RAY DIFFRACTIONr_mcangle_it6.7639.182499
X-RAY DIFFRACTIONr_mcangle_other6.7639.1822500
X-RAY DIFFRACTIONr_scbond_it6.2625.7821877
X-RAY DIFFRACTIONr_scbond_other5.9435.681846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.80910.1492759
X-RAY DIFFRACTIONr_long_range_B_refined10.83848.14114
X-RAY DIFFRACTIONr_long_range_B_other10.78148.114114
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 111 -
Rwork0.335 1927 -
obs--99.95 %

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