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- PDB-6xrc: Apo NIS synthetase DesD variant R306Q -

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Basic information

Entry
Database: PDB / ID: 6xrc
TitleApo NIS synthetase DesD variant R306Q
ComponentsDesferrioxamine E biosynthesis protein DesD
KeywordsBIOSYNTHETIC PROTEIN / NIS synthetase / catalytic variant / siderophore synthesis
Function / homologyAerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter / acid-amino acid ligase activity / siderophore biosynthetic process / ADENOSINE-5'-TRIPHOSPHATE / Uncharacterized protein
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHoffmann, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1716986 United States
CitationJournal: Biochemistry / Year: 2020
Title: Cofactor Complexes of DesD, a Model Enzyme in the Virulence-related NIS Synthetase Family.
Authors: Hoffmann, K.M. / Goncuian, E.S. / Karimi, K.L. / Amendola, C.R. / Mojab, Y. / Wood, K.M. / Prussia, G.A. / Nix, J. / Yamamoto, M. / Lathan, K. / Orion, I.W.
History
DepositionJul 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: 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: Desferrioxamine E biosynthesis protein DesD
B: Desferrioxamine E biosynthesis protein DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,77610
Polymers135,4132
Non-polymers1,3648
Water11,530640
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-71 kcal/mol
Surface area42800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.417, 98.921, 183.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Desferrioxamine E biosynthesis protein DesD


Mass: 67706.320 Da / Num. of mol.: 2 / Mutation: R306Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO2785 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L069
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 640 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.08 mM Tris-HCl, pH 8.5, 160 mM magnesium chloride, 24% PEG4000, 20% glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 30, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→61.12 Å / Num. obs: 50570 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.063 / Rrim(I) all: 0.172 / Χ2: 0.98 / Net I/σ(I): 7.7
Reflection shellResolution: 2.45→2.53 Å / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4574 / CC1/2: 0.964 / Χ2: 0.74

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NL2

6nl2


Resolution: 2.45→59.47 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: FREE R-VALUE / ESU R: 0.207 / ESU R Free: 0.099
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.27 2494 4.936 %
Rwork0.2 --
obs-50526 99.8 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.18 Å2
Baniso -1Baniso -2Baniso -3
1--8.804 Å20 Å20 Å2
2--34.526 Å20 Å2
3----25.721 Å2
Refinement stepCycle: LAST / Resolution: 2.45→59.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9354 0 83 640 10077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0139695
X-RAY DIFFRACTIONr_bond_other_d0.0350.0178870
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.64313214
X-RAY DIFFRACTIONr_angle_other_deg2.41.56920445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.05551198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00920.912548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83151510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0091586
X-RAY DIFFRACTIONr_chiral_restr0.080.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210996
X-RAY DIFFRACTIONr_gen_planes_other0.0120.022204
X-RAY DIFFRACTIONr_nbd_refined0.2140.22156
X-RAY DIFFRACTIONr_nbd_other0.2260.241
X-RAY DIFFRACTIONr_nbtor_refined0.1710.24567
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2593
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5043.4924768
X-RAY DIFFRACTIONr_mcbond_other1.5023.4914766
X-RAY DIFFRACTIONr_mcangle_it2.6075.2355959
X-RAY DIFFRACTIONr_mcangle_other2.6055.2355959
X-RAY DIFFRACTIONr_scbond_it1.683.5554927
X-RAY DIFFRACTIONr_scbond_other1.6793.5554927
X-RAY DIFFRACTIONr_scangle_it2.7815.2817250
X-RAY DIFFRACTIONr_scangle_other2.785.2817251
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.51 Å
Num. reflection% reflection
Rfree183 -
Rwork3503 -
obs-99.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.95260.2250.2590.38140.36551.83010.02050.0801-0.1130.0545-0.0109-0.00180.05860.0432-0.00970.11960.0090.00520.02120.0150.093616.58926.47320.652
21.0079-0.25830.26440.389-0.29121.8447-0.0452-0.0322-0.1061-0.05230.0142-0.00580.03620.00550.0310.1074-0.00120.01670.0032-0.00910.097420.65526.766.926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 596
2X-RAY DIFFRACTION2B2 - 596

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