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- PDB-5n9x: Structure of adenylation domain THR1 involved in the biosynthesis... -

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Basic information

Entry
Database: PDB / ID: 5n9x
TitleStructure of adenylation domain THR1 involved in the biosynthesis of 4-chlorothreonine in Streptomyces SP.OH-5093, ligand bound structure
ComponentsAdenylation domain
KeywordsLIGASE / adenylation domain / substrate specificity / non-ribosomal code / threonine adenylate
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / catalytic activity / ATP binding / cytoplasm
Similarity search - Function
AMP-binding / ANL, C-terminal domain / ANL, N-terminal domain / Amino acid adenylation domain / 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. / GMP Synthetase; Chain A, domain 3 ...AMP-binding / ANL, C-terminal domain / ANL, N-terminal domain / Amino acid adenylation domain / 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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8QN / ADENOSINE-5'-TRIPHOSPHATE / THREONINE / Adenylation domain
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å
AuthorsSavino, C. / Vallone, B. / Scaglione, A. / Parisi, G. / Montemiglio, L.C. / Fullone, M.R. / Grgurina, I.
CitationJournal: FEBS J. / Year: 2017
Title: Structure of the adenylation domain Thr1 involved in the biosynthesis of 4-chlorothreonine in Streptomyces sp. OH-5093-protein flexibility and molecular bases of substrate specificity.
Authors: Scaglione, A. / Fullone, M.R. / Montemiglio, L.C. / Parisi, G. / Zamparelli, C. / Vallone, B. / Savino, C. / Grgurina, I.
History
DepositionFeb 27, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionJul 26, 2017ID: 5APB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Adenylation domain
B: Adenylation domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5496
Polymers115,4502
Non-polymers1,0994
Water3,549197
1
A: Adenylation domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3764
Polymers57,7251
Non-polymers6513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylation domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1732
Polymers57,7251
Non-polymers4481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.022, 52.524, 110.119
Angle α, β, γ (deg.)90.00, 105.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Adenylation domain


Mass: 57724.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: thr1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6SG27

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Non-polymers , 5 types, 201 molecules

#2: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-8QN / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S},3~{R})-2-azanyl-3-oxidanyl-butanoate


Mass: 448.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N6O9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0,1M HEPES 10% v/v isopropanol 20% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.396→50 Å / Num. obs: 69955 / % possible obs: 92 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.4
Reflection shellResolution: 2.396→2.54 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.39 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIXdev_1647refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VNQ

3vnq


Resolution: 2.396→46.867 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 28.27
RfactorNum. reflection% reflection
Rfree0.2755 3484 4.99 %
Rwork0.1993 --
obs0.2031 69868 92.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.396→46.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7516 0 70 197 7783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097893
X-RAY DIFFRACTIONf_angle_d1.35810777
X-RAY DIFFRACTIONf_dihedral_angle_d16.6732890
X-RAY DIFFRACTIONf_chiral_restr0.0541210
X-RAY DIFFRACTIONf_plane_restr0.0081407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3959-2.42870.29141120.22842149X-RAY DIFFRACTION77
2.4287-2.46340.32631360.22952649X-RAY DIFFRACTION91
2.4634-2.50020.33261490.22752837X-RAY DIFFRACTION96
2.5002-2.53930.33981450.2112746X-RAY DIFFRACTION97
2.5393-2.58090.28671510.22352755X-RAY DIFFRACTION96
2.5809-2.62540.31161450.22052794X-RAY DIFFRACTION96
2.6254-2.67310.29341390.22512724X-RAY DIFFRACTION96
2.6731-2.72450.31871450.22852773X-RAY DIFFRACTION96
2.7245-2.78010.33661450.22432726X-RAY DIFFRACTION95
2.7801-2.84060.34171400.21962744X-RAY DIFFRACTION94
2.8406-2.90660.28761480.21952755X-RAY DIFFRACTION96
2.9066-2.97930.32091460.22342716X-RAY DIFFRACTION95
2.9793-3.05990.25411470.21332747X-RAY DIFFRACTION94
3.0599-3.14990.32941350.20992645X-RAY DIFFRACTION93
3.1499-3.25150.30931390.22672705X-RAY DIFFRACTION93
3.2515-3.36770.35961360.21252614X-RAY DIFFRACTION92
3.3677-3.50250.30371400.22272612X-RAY DIFFRACTION90
3.5025-3.66190.23791310.20992535X-RAY DIFFRACTION89
3.6619-3.85480.30661350.19652533X-RAY DIFFRACTION88
3.8548-4.09620.23031290.18552543X-RAY DIFFRACTION88
4.0962-4.41230.24261360.16552594X-RAY DIFFRACTION89
4.4123-4.85590.22041290.15772492X-RAY DIFFRACTION88
4.8559-5.55760.22921440.15992612X-RAY DIFFRACTION91
5.5576-6.99820.2581370.18942636X-RAY DIFFRACTION92
6.9982-46.87550.18421450.16922748X-RAY DIFFRACTION95

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