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- PDB-6ulx: Adenylation domain of a keto acid-selecting NRPS module bound to ... -

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Basic information

Entry
Database: PDB / ID: 6ulx
TitleAdenylation domain of a keto acid-selecting NRPS module bound to keto acyl adenylate space group P43212
ComponentsAmino acid adenylation domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / NRPS / Nonribosomal peptide synthetase / non-ribosomal peptide synthetase / adenylation / adenylation domain / depsipeptide / cereulide / valinomycin / natural product / adenylate / keto acid / ketoacid
Function / homology
Function and homology information


ligase activity / phosphopantetheine binding / antibiotic biosynthetic process
Similarity search - Function
Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, ketoreductase domain / KR domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site ...Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, ketoreductase domain / KR domain / ANL, N-terminal 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 / PKS_KR / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-QA7 / Amino acid adenylation domain-containing protein
Similarity search - Component
Biological speciesBacillus stratosphericus LAMA 585 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsAlonzo, D.A. / Chiche-Lapierre, C. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Citation
Journal: Nat.Chem.Biol. / Year: 2020
Title: Structural basis of keto acid utilization in nonribosomal depsipeptide synthesis.
Authors: Alonzo, D.A. / Chiche-Lapierre, C. / Tarry, M.J. / Wang, J. / Schmeing, T.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
#3: Journal: J Appl Crystallogr / Year: 2007
Title: Phaser crystallographic software.
Authors: McCoy, A.J. / Grosse-Kunstleve, R.W. / Adams, P.D. / Winn, M.D. / Storoni, L.C. / Read, R.J.
History
DepositionOct 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 6, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Amino acid adenylation domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,02919
Polymers63,9361
Non-polymers2,09218
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-219 kcal/mol
Surface area24510 Å2
Unit cell
Length a, b, c (Å)103.274, 103.274, 172.747
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-573-

CYS

21A-853-

HOH

31A-859-

HOH

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Components

#1: Protein Amino acid adenylation domain-containing protein / WP_007498213


Mass: 63936.355 Da / Num. of mol.: 1 / Fragment: first adenylation domain (UNP residues 83-649)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus stratosphericus LAMA 585 (bacteria)
Gene: C883_1060 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M5R382
#2: Chemical ChemComp-QA7 / 5'-O-{(S)-hydroxy[(4-methyl-2-oxopentanoyl)oxy]phosphoryl}adenosine


Mass: 459.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22N5O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.75 Å3/Da / Density % sol: 67.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.75 M ammonium sulfate, 22.5% v/v glycerol, 3% w/v trimethylamine N-oxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2019
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→88.42 Å / Num. obs: 41902 / % possible obs: 99.8 % / Redundancy: 13.2 % / Biso Wilson estimate: 43.67 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.045 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4027 / CC1/2: 0.778 / Rpim(I) all: 0.593

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→73.03 Å / SU ML: 0.2767 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4049
RfactorNum. reflection% reflection
Rfree0.2491 1905 4.56 %
Rwork0.2216 --
obs0.2228 41750 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 63.64 Å2
Refinement stepCycle: LAST / Resolution: 2.31→73.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 116 59 4471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414495
X-RAY DIFFRACTIONf_angle_d0.576119
X-RAY DIFFRACTIONf_chiral_restr0.0427677
X-RAY DIFFRACTIONf_plane_restr0.0032772
X-RAY DIFFRACTIONf_dihedral_angle_d13.73312603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.360.34411340.30792782X-RAY DIFFRACTION99.02
2.36-2.430.31151320.28872785X-RAY DIFFRACTION99.12
2.43-2.50.31831330.26952770X-RAY DIFFRACTION99.18
2.5-2.580.30821350.26452806X-RAY DIFFRACTION99.12
2.58-2.670.26171320.24962790X-RAY DIFFRACTION99.62
2.67-2.780.29371360.24082818X-RAY DIFFRACTION99.53
2.78-2.90.29111330.23812778X-RAY DIFFRACTION98.48
2.9-3.060.2631350.23832848X-RAY DIFFRACTION99.63
3.06-3.250.27591350.2412838X-RAY DIFFRACTION99.97
3.25-3.50.27281370.22992848X-RAY DIFFRACTION99.93
3.5-3.850.24841370.20992883X-RAY DIFFRACTION99.93
3.85-4.410.22341380.19212871X-RAY DIFFRACTION99.57
4.41-5.560.19131400.18632936X-RAY DIFFRACTION100
5.56-73.030.23361480.22023092X-RAY DIFFRACTION99.6

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