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- PDB-8p5o: Proline activating adenylation domain of gramicidin S synthetase ... -

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Basic information

Entry
Database: PDB / ID: 8p5o
TitleProline activating adenylation domain of gramicidin S synthetase 2 - GrsB1-Acore
ComponentsGramicidin S synthase 2
KeywordsBIOSYNTHETIC PROTEIN / Nonribosomal Peptide Synthetase / Adenylation domain
Function / homology
Function and homology information


amide biosynthetic process / organonitrogen compound biosynthetic process / secondary metabolite biosynthetic process / carboxylic acid metabolic process / phosphopantetheine binding / ligase activity / antibiotic biosynthetic process / hydrolase activity
Similarity search - Function
Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. ...Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Gramicidin S synthase 2
Similarity search - Component
Biological speciesAneurinibacillus migulanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsStephan, P. / Basquin, J. / Caputi, L. / O'Connor, S.E. / Kries, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other private Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Directed Evolution of Piperazic Acid Incorporation by a Nonribosomal Peptide Synthetase.
Authors: Stephan, P. / Langley, C. / Winkler, D. / Basquin, J. / Caputi, L. / O'Connor, S.E. / Kries, H.
History
DepositionMay 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gramicidin S synthase 2
B: Gramicidin S synthase 2
C: Gramicidin S synthase 2
D: Gramicidin S synthase 2


Theoretical massNumber of molelcules
Total (without water)187,7534
Polymers187,7534
Non-polymers00
Water86548
1
A: Gramicidin S synthase 2


Theoretical massNumber of molelcules
Total (without water)46,9381
Polymers46,9381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gramicidin S synthase 2


Theoretical massNumber of molelcules
Total (without water)46,9381
Polymers46,9381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Gramicidin S synthase 2


Theoretical massNumber of molelcules
Total (without water)46,9381
Polymers46,9381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Gramicidin S synthase 2


Theoretical massNumber of molelcules
Total (without water)46,9381
Polymers46,9381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)195.021, 195.021, 346.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein
Gramicidin S synthase 2 / Gramicidin S synthase II


Mass: 46938.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aneurinibacillus migulanus (bacteria) / Gene: grsB, grs2 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: P0C063
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000, 312mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→60.46 Å / Num. obs: 77790 / % possible obs: 99.95 % / Redundancy: 10.5 % / Biso Wilson estimate: 68.28 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.86
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 7694 / CC1/2: 0.434

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Processing

Software
NameVersionClassification
PHENIX1.19rc6_4061refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→60.46 Å / SU ML: 0.392 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3187
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2487 3889 2.56 %
Rwork0.2232 147891 -
obs0.2238 77790 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→60.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12807 0 0 48 12855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002413108
X-RAY DIFFRACTIONf_angle_d0.499317753
X-RAY DIFFRACTIONf_chiral_restr0.04421961
X-RAY DIFFRACTIONf_plane_restr0.0042299
X-RAY DIFFRACTIONf_dihedral_angle_d18.22934915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.36371380.34765184X-RAY DIFFRACTION99.72
2.63-2.660.37751390.3345324X-RAY DIFFRACTION99.96
2.66-2.70.34611350.33435243X-RAY DIFFRACTION99.87
2.7-2.730.34431420.34055354X-RAY DIFFRACTION99.95
2.73-2.770.371370.32645255X-RAY DIFFRACTION99.98
2.77-2.810.34131420.31335293X-RAY DIFFRACTION100
2.81-2.860.33011400.31875248X-RAY DIFFRACTION100
2.86-2.90.35291410.31135326X-RAY DIFFRACTION100
2.9-2.950.29661370.29385277X-RAY DIFFRACTION100
2.95-3.010.29751420.27515256X-RAY DIFFRACTION100
3.01-3.070.30781380.27415291X-RAY DIFFRACTION100
3.07-3.130.3141380.26115317X-RAY DIFFRACTION99.98
3.13-3.20.28931420.24945278X-RAY DIFFRACTION100
3.2-3.270.28321330.24375261X-RAY DIFFRACTION99.98
3.27-3.350.33311410.25335296X-RAY DIFFRACTION99.91
3.35-3.440.25921370.24185266X-RAY DIFFRACTION99.91
3.44-3.540.26111390.24115286X-RAY DIFFRACTION99.76
3.54-3.660.25941390.22765295X-RAY DIFFRACTION99.98
3.66-3.790.26741380.2265277X-RAY DIFFRACTION100
3.79-3.940.28131400.21075284X-RAY DIFFRACTION99.98
3.94-4.120.20061380.20035241X-RAY DIFFRACTION100
4.12-4.340.24731450.19075333X-RAY DIFFRACTION100
4.34-4.610.19351370.19155284X-RAY DIFFRACTION100
4.61-4.960.17841360.18285299X-RAY DIFFRACTION100
4.96-5.460.20281360.20485256X-RAY DIFFRACTION100
5.46-6.250.26471400.22835302X-RAY DIFFRACTION100
6.25-7.870.29021420.21855268X-RAY DIFFRACTION99.76
7.88-60.460.17321370.16885297X-RAY DIFFRACTION99.67

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