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- PDB-7tgk: Crystal structure of ATP bound DesD, the desferrioxamine syntheta... -

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Basic information

Entry
Database: PDB / ID: 7tgk
TitleCrystal structure of ATP bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway
ComponentsDesferrioxamine synthetase DesD
KeywordsLIGASE / NRPS-independent siderophore (NIS) synthetase / iterative synthetase / amide ligase / adenylate-forming enzyme
Function / homologyADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPatel, K.D. / Gulick, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136235 United States
National Science Foundation (NSF, United States)1654611 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD.
Authors: Yang, J. / Banas, V.S. / Patel, K.D. / Rivera, G.S.M. / Mydy, L.S. / Gulick, A.M. / Wencewicz, T.A.
History
DepositionJan 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Desferrioxamine synthetase DesD
B: Desferrioxamine synthetase DesD
E: Desferrioxamine synthetase DesD
A: Desferrioxamine synthetase DesD
C: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,12570
Polymers343,8085
Non-polymers8,31865
Water14,538807
1
D: Desferrioxamine synthetase DesD
C: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,13529
Polymers137,5232
Non-polymers3,61227
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Desferrioxamine synthetase DesD
A: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,97830
Polymers137,5232
Non-polymers3,45528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Desferrioxamine synthetase DesD
hetero molecules

E: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,02422
Polymers137,5232
Non-polymers2,50120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)126.407, 237.528, 326.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11E-768-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 41 or (resid 42...
d_2ens_1(chain "B" and (resid 0 through 207 or (resid 208...
d_3ens_1(chain "C" and (resid 0 through 43 or (resid 44...
d_4ens_1(chain "D" and (resid 0 through 41 or (resid 42...
d_5ens_1(chain "E" and (resid 0 through 43 or (resid 44...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISGLYD1 - 592
d_21ens_1HISGLYB1 - 592
d_31ens_1HISGLYE1 - 592
d_41ens_1HISGLYA1 - 592
d_51ens_1HISGLYC1 - 592

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Components

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Protein , 1 types, 5 molecules DBEAC

#1: Protein
Desferrioxamine synthetase DesD


Mass: 68761.516 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 6 types, 872 molecules

#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 807 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.57 Å3/Da / Density % sol: 65.53 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05M BTP pH 7.0, 0.2M Ammonium sulfate 16% PEG 4000 (under oil 100%)

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→49 Å / Num. obs: 216739 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 50.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.04 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 250917 / CC1/2: 0.627 / Rpim(I) all: 0.55

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unliganded FerDesD 7TGJ

7tgj


Resolution: 2.3→48.95 Å / SU ML: 0.2793 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2162 1976 0.91 %
Rwork0.1828 214667 -
obs0.1831 216643 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23426 0 481 808 24715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014524427
X-RAY DIFFRACTIONf_angle_d1.245533319
X-RAY DIFFRACTIONf_chiral_restr0.06233636
X-RAY DIFFRACTIONf_plane_restr0.00864292
X-RAY DIFFRACTIONf_dihedral_angle_d9.33763383
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DX-RAY DIFFRACTIONTorsion NCS0.546181362366
ens_1d_3DX-RAY DIFFRACTIONTorsion NCS0.591259193129
ens_1d_4DX-RAY DIFFRACTIONTorsion NCS0.604214576651
ens_1d_5DX-RAY DIFFRACTIONTorsion NCS0.570956424366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.28541240.267415156X-RAY DIFFRACTION99.16
2.36-2.420.27561530.249115165X-RAY DIFFRACTION99.92
2.42-2.490.30941440.240615270X-RAY DIFFRACTION99.91
2.49-2.570.27791380.230115207X-RAY DIFFRACTION99.98
2.57-2.660.2731410.229415261X-RAY DIFFRACTION99.95
2.66-2.770.27221350.215915252X-RAY DIFFRACTION99.97
2.77-2.90.22691460.210515287X-RAY DIFFRACTION99.97
2.9-3.050.25471420.211315273X-RAY DIFFRACTION99.87
3.05-3.240.29031430.221615324X-RAY DIFFRACTION99.96
3.24-3.490.23591370.19415312X-RAY DIFFRACTION99.98
3.49-3.840.19921430.171615417X-RAY DIFFRACTION99.9
3.84-4.40.1521450.14415387X-RAY DIFFRACTION99.92
4.4-5.540.15931460.147815486X-RAY DIFFRACTION99.9
5.54-48.950.2341390.172815870X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: 82.3981125971 Å / Origin y: 45.3697109472 Å / Origin z: -42.9354161498 Å
111213212223313233
T0.38484772708 Å20.0573583173868 Å2-0.0349749701764 Å2-0.418738384631 Å2-0.0273326591014 Å2--0.38555192313 Å2
L0.0555746186989 °20.0613316386641 °2-0.0129887783784 °2-0.228318564011 °2-0.0766262455582 °2--0.0924206569549 °2
S0.0110787188261 Å °-0.0431318083587 Å °0.0084763465875 Å °0.0357776163591 Å °0.0037050692485 Å °-0.0142252217874 Å °-0.0316665940321 Å °-0.000132317929064 Å °-0.0147484782501 Å °
Refinement TLS groupSelection details: all

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