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

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Basic information

Entry
Database: PDB / ID: 8ppp
TitleAmide bond synthetase from Streptomyces hindustanus K492H mutant in complex with AMP-CPP
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, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Fatty-acyl-CoA synthase
Similarity search - Component
Biological speciesStreptoalloteichus hindustanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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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)109,0564
Polymers108,0462
Non-polymers1,0102
Water6,179343
1
A: Fatty-acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5282
Polymers54,0231
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty-acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5282
Polymers54,0231
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.700, 95.700, 87.200
Angle α, β, γ (deg.)90.00, 117.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fatty-acyl-CoA synthase /


Mass: 54022.930 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 BL21(DE3) (bacteria) / References: UniProt: A0A1M5ABR5
#2: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.83 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M lithium sulfate; 0.1 M HEPES pH 7.5; 25% PEG (w/v) 3350; 4 deg C.

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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: 2.57→58.19 Å / Num. obs: 38357 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 2.57→2.68 Å / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4648 / CC1/2: 0.83 / Rpim(I) all: 0.67

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→58.19 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.669 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.69 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27554 1994 5.2 %RANDOM
Rwork0.2112 ---
obs0.21455 36345 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-1.18 Å2
2--4.05 Å2-0 Å2
3----1.55 Å2
Refinement stepCycle: 1 / Resolution: 2.57→58.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 0 62 359 7813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127630
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167143
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.65310456
X-RAY DIFFRACTIONr_angle_other_deg0.4761.56516367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.595563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.452101089
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.21223
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029095
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021671
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_it3.5833.9163992
X-RAY DIFFRACTIONr_mcbond_other3.5793.9173992
X-RAY DIFFRACTIONr_mcangle_it5.5587.0234984
X-RAY DIFFRACTIONr_mcangle_other5.5587.0244985
X-RAY DIFFRACTIONr_scbond_it4.0874.2583638
X-RAY DIFFRACTIONr_scbond_other4.0864.2593639
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4217.6915471
X-RAY DIFFRACTIONr_long_range_B_refined8.7638.848623
X-RAY DIFFRACTIONr_long_range_B_other8.76238.688590
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 168 -
Rwork0.322 2653 -
obs--99.86 %

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