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- PDB-6ulw: Adenylation, ketoreductase, and pseudo Asub multidomain structure... -

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Basic information

Entry
Database: PDB / ID: 6ulw
TitleAdenylation, ketoreductase, and pseudo Asub multidomain structure of a keto acid-selecting NRPS module
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 / ketoreductase / short chain dehydrogenase
Function / homology
Function and homology information


ligase activity / phosphopantetheine binding / antibiotic biosynthetic process
Similarity search - Function
Non-ribosomal peptide synthase / ANL, N-terminal domain / 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 ...Non-ribosomal peptide synthase / ANL, N-terminal domain / 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. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Amino acid adenylation domain-containing protein
Similarity search - Component
Biological speciesBacillus stratosphericus LAMA 585 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsAlonzo, D.A. / Wang, J. / Chiche-Lapierre, C. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: 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.
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 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amino acid adenylation domain-containing protein
B: Amino acid adenylation domain-containing protein
C: Amino acid adenylation domain-containing protein
D: Amino acid adenylation domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)596,06713
Polymers595,7224
Non-polymers3459
Water00
1
A: Amino acid adenylation domain-containing protein
C: Amino acid adenylation domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,0216
Polymers297,8612
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-81 kcal/mol
Surface area102700 Å2
MethodPISA
2
B: Amino acid adenylation domain-containing protein
D: Amino acid adenylation domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,0467
Polymers297,8612
Non-polymers1855
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-92 kcal/mol
Surface area102290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.660, 143.660, 431.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: GLU / End label comp-ID: GLU

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSER(chain 'A' and (resid 14 through 193 or (resid 194...AA14 - 6114 - 61
12PROPRO(chain 'A' and (resid 14 through 193 or (resid 194...AA83 - 122583 - 1225
23SERSER(chain 'B' and (resid 14 through 61 or resid 83...BB14 - 6114 - 61
24PROPRO(chain 'B' and (resid 14 through 61 or resid 83...BB83 - 122583 - 1225
35SERSER(chain 'C' and (resid 14 through 61 or resid 83...CC14 - 6114 - 61
36PROPRO(chain 'C' and (resid 14 through 61 or resid 83...CC83 - 122583 - 1225
47SERSER(chain 'D' and (resid 14 through 186 or (resid 187...DD14 - 6114 - 61
48PROPRO(chain 'D' and (resid 14 through 186 or (resid 187...DD83 - 122583 - 1225

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Components

#1: Protein
Amino acid adenylation domain-containing protein


Mass: 148930.547 Da / Num. of mol.: 4
Fragment: adenylation, ketoreductase, and pseudo Asub domains (UNP residues 1-1318)
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 3.69 Å3/Da / Density % sol: 66.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.165 M sodium succinate, 0.24 % v/v PEG2000 MME, 0.02 M HEPES, 0.016 M sodium chloride, 5.9% v/v PEG3350, 0.104 M calcium acetate, 0.01 M phenol
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2017
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.4→100 Å / Num. obs: 121921 / % possible obs: 98 % / Redundancy: 3.5 % / Biso Wilson estimate: 141.68 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.123 / Net I/σ(I): 8.86
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 0.33 / Num. unique obs: 15106 / CC1/2: 0.136 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1

4r0m

4iz6

4dg8

3tsy

3kxw

3g7s

3etc

2vsq

5d2e

4l4x

4j1q

4imp

4hxy

3slk

3qp9

3mjt

2z5l

2fr1


Resolution: 3.4→49.11 Å / SU ML: 0.6557 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.8326
RfactorNum. reflection% reflection
Rfree0.275 5958 4.96 %
Rwork0.2276 --
obs0.2299 120166 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 181.88 Å2
Refinement stepCycle: LAST / Resolution: 3.4→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37831 0 9 0 37840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00438701
X-RAY DIFFRACTIONf_angle_d0.679852449
X-RAY DIFFRACTIONf_chiral_restr0.04415841
X-RAY DIFFRACTIONf_plane_restr0.00436757
X-RAY DIFFRACTIONf_dihedral_angle_d20.741323123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.440.48981740.45063253X-RAY DIFFRACTION85.27
3.44-3.480.46851920.43783514X-RAY DIFFRACTION91.82
3.48-3.520.44691820.4243768X-RAY DIFFRACTION99.07
3.52-3.570.43911720.39963794X-RAY DIFFRACTION99.57
3.57-3.610.39682020.36723837X-RAY DIFFRACTION99.56
3.61-3.660.38112170.36923758X-RAY DIFFRACTION99.08
3.66-3.710.40181950.36663780X-RAY DIFFRACTION99.6
3.71-3.770.37232360.33473788X-RAY DIFFRACTION99.55
3.77-3.830.3532100.30833801X-RAY DIFFRACTION99.55
3.83-3.890.36532080.30773791X-RAY DIFFRACTION99.58
3.89-3.960.35471730.30073859X-RAY DIFFRACTION99.73
3.96-4.030.30871750.27713821X-RAY DIFFRACTION99.63
4.03-4.110.37361550.27453876X-RAY DIFFRACTION99.63
4.11-4.190.34222020.26663775X-RAY DIFFRACTION98.78
4.19-4.280.30851970.24683821X-RAY DIFFRACTION99.75
4.28-4.380.29691960.24413835X-RAY DIFFRACTION99.68
4.38-4.490.28811850.22923855X-RAY DIFFRACTION99.78
4.49-4.610.24141770.21113824X-RAY DIFFRACTION99.65
4.61-4.750.23462100.20183830X-RAY DIFFRACTION99.8
4.75-4.90.24572140.2093843X-RAY DIFFRACTION99.78
4.9-5.080.27912180.21393815X-RAY DIFFRACTION99.24
5.08-5.280.26962500.21773744X-RAY DIFFRACTION98.3
5.28-5.520.27962110.22363855X-RAY DIFFRACTION99.75
5.52-5.810.28541830.22123873X-RAY DIFFRACTION99.68
5.81-6.170.28081580.22913935X-RAY DIFFRACTION99.8
6.17-6.650.28661960.2313876X-RAY DIFFRACTION99.63
6.65-7.320.27722340.22163806X-RAY DIFFRACTION97.82
7.32-8.370.2742100.2093943X-RAY DIFFRACTION99.83
8.37-10.530.19461990.14863883X-RAY DIFFRACTION97.7
10.53-49.110.21752270.18414055X-RAY DIFFRACTION97.76

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