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- PDB-5n9w: Structure of adenylation domain THR1 involved in the biosynthesis... -

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Basic information

Entry
Database: PDB / ID: 5n9w
TitleStructure of adenylation domain THR1 involved in the biosynthesis of 4-chlorothreonine in Streptomyces SP.OH-5093, apo structure
ComponentsAdenylation domainAdenylylation
KeywordsTRANSFERASE / adenylation domain / substrate specificity / non-ribosomal code
Function / homology
Function and homology information


antibiotic biosynthetic process / ATP binding
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, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Adenylation domain
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.456 Å
AuthorsSavino, C. / Vallone, B. / Scaglione, A. / Parisi, G. / Montemiglio, L.C. / Fullone, M.R. / Grgurina, I.
Funding support Italy, 2items
OrganizationGrant numberCountry
Sapienza University of RomeC26A14P4BP Italy
Regione Lazio ProToxFILAS-RU-2014-1020 Italy
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: 5APL
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)115,6275
Polymers115,4502
Non-polymers1773
Water1,62190
1
A: Adenylation domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7842
Polymers57,7251
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylation domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8433
Polymers57,7251
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)177.633, 52.806, 108.861
Angle α, β, γ (deg.)90.00, 105.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Adenylation domain / Adenylylation


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
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 38.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0,2M Magnesium Acetate 0,1M Sodium Cacodylate 20% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.456→50 Å / Num. obs: 35853 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12
Reflection shellResolution: 2.456→2.6 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.25 / % possible all: 98.5

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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: 2.456→46.955 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.85
RfactorNum. reflection% reflection
Rfree0.2699 1793 5 %
Rwork0.1973 --
obs0.2009 35843 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.456→46.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7353 0 12 90 7455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097544
X-RAY DIFFRACTIONf_angle_d1.20510269
X-RAY DIFFRACTIONf_dihedral_angle_d16.6692743
X-RAY DIFFRACTIONf_chiral_restr0.0511156
X-RAY DIFFRACTIONf_plane_restr0.0071347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4558-2.52210.38841340.27462543X-RAY DIFFRACTION97
2.5221-2.59640.34221350.24492575X-RAY DIFFRACTION100
2.5964-2.68020.31261380.23542620X-RAY DIFFRACTION100
2.6802-2.77590.34551370.25092589X-RAY DIFFRACTION100
2.7759-2.88710.30931370.23672600X-RAY DIFFRACTION100
2.8871-3.01840.32771360.24812597X-RAY DIFFRACTION100
3.0184-3.17750.29881390.23122627X-RAY DIFFRACTION100
3.1775-3.37660.32981370.2112606X-RAY DIFFRACTION100
3.3766-3.63720.23571380.19012620X-RAY DIFFRACTION100
3.6372-4.0030.25261390.17572639X-RAY DIFFRACTION100
4.003-4.58190.22171380.15252640X-RAY DIFFRACTION100
4.5819-5.7710.23371410.16592660X-RAY DIFFRACTION100
5.771-46.96330.23221440.18352734X-RAY DIFFRACTION100

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