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- PDB-8pyx: Amide bond synthetase from Streptomyces hindustanus K492H mutant ... -

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Basic information

Entry
Database: PDB / ID: 8pyx
TitleAmide bond synthetase from Streptomyces hindustanus K492H mutant in complex with Adenosine
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
ADENOSINE / Fatty-acyl-CoA synthase
Similarity search - Component
Biological speciesStreptoalloteichus hindustanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,01210
Polymers108,9012
Non-polymers1,1118
Water9,116506
1
A: Fatty-acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0065
Polymers54,4501
Non-polymers5554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty-acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0065
Polymers54,4501
Non-polymers5554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.167, 96.159, 87.323
Angle α, β, γ (deg.)90.00, 117.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fatty-acyl-CoA synthase / Amide bond synthetase / Amide ligase


Mass: 54450.410 Da / Num. of mol.: 2 / Mutation: K492H
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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Li2SO4; 0.1 M HEPES pH 7.5; 25% PEG 3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.95881 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95881 Å / Relative weight: 1
ReflectionResolution: 2.02→29.35 Å / Num. obs: 78528 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.06 / Net I/σ(I): 11.6
Reflection shellResolution: 2.02→2.06 Å / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3766 / CC1/2: 0.8 / Rpim(I) all: 0.55

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→29.35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.316 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26231 3938 5 %RANDOM
Rwork0.22442 ---
obs0.22632 74561 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.238 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å2-0.11 Å2
2--1.69 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 2.02→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7393 0 68 513 7974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127638
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167142
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.64910460
X-RAY DIFFRACTIONr_angle_other_deg0.4691.56416381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.673562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.542101089
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.21221
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021668
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_it2.7013.123974
X-RAY DIFFRACTIONr_mcbond_other2.73.123974
X-RAY DIFFRACTIONr_mcangle_it3.7595.5894959
X-RAY DIFFRACTIONr_mcangle_other3.7595.5894960
X-RAY DIFFRACTIONr_scbond_it3.1563.4593664
X-RAY DIFFRACTIONr_scbond_other3.143.443641
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7726.1865462
X-RAY DIFFRACTIONr_long_range_B_refined6.24232.818475
X-RAY DIFFRACTIONr_long_range_B_other6.232.128367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.068 Å
RfactorNum. reflection% reflection
Rfree0.363 277 -
Rwork0.329 4819 -
obs--87.23 %

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